3TNQ | pdb_00003tnq

Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d3tnqb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	cAMP-dependent PK, catalytic subunit	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2 Family	Protein kinases catalytic domain-like	8069144	4003661	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	Protein kinase-like (PK-like)	8069145	3000066	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	zf-MYND	e3tnqA2	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (develop294)
B [auth A]	DUF3228	e3tnqA4	A: alpha bundles	X: POZ domain	H: POZ domain	T: POZ domain	F: DUF3228	ECOD (develop294)
A [auth B]	Flu_NP	e3tnqB2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Flu_NP	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
A [auth B]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
A [auth B]	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF00027	Cyclic nucleotide-binding domain (cNMP_binding)	Cyclic nucleotide-binding domain	This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A [auth B]	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	cAMP-dependent protein kinase type II-beta regulatory subunit	protein binding binding protein domain specific binding enzyme regulator activity enzyme inhibitor activity protein kinase regulator activity cAMP-dependent protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity cAMP-dependent protein kinase inhibitor activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity protein binding binding protein domain specific binding enzyme regulator activity enzyme inhibitor activity protein kinase regulator activity cAMP-dependent protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity cAMP-dependent protein kinase inhibitor activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity kinase binding enzyme binding protein kinase binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein kinase A catalytic subunit binding protein kinase A binding	behavior multicellular organismal process system process learning learning or memory nervous system process cognition cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation adenylate cyclase-activating G protein-coupled receptor signaling pathway behavior multicellular organismal process system process learning learning or memory nervous system process cognition cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation adenylate cyclase-activating G protein-coupled receptor signaling pathway cell communication adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cellular process signal transduction fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lipid metabolic process trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cAMP/PKA signal transduction intracellular signal transduction negative regulation of cell communication cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction regulation of cAMP/PKA signal transduction regulation of response to stimulus response to antipsychotic drug response to chemical	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol cell periphery plasma membrane intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse dendritic shaft neuron spine dendritic spine postsynapse perinuclear region of cytoplasm cell body neuronal cell body ciliary base membrane-bounded organelle cilium protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cAMP-dependent protein kinase complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex
A [auth B]	Protein kinase, cAMP-dependent, catalytic, alpha	small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H1 kinase activity histone H1-4S35 kinase activity small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H1 kinase activity histone H1-4S35 kinase activity histone modifying activity catalytic activity histone kinase activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein domain specific binding protein serine/threonine/tyrosine kinase activity cyclic nucleotide-dependent protein kinase activity cAMP-dependent protein kinase activity protein serine kinase activity magnesium ion binding kinase binding protein kinase binding protein kinase A binding protein kinase A regulatory subunit binding	developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation anatomical structure maturation cell differentiation anatomical structure development germ cell development cellular process cell maturation cellular localization establishment of protein localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization nuclear export intracellular protein transport cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus cellular response to nutrient levels response to nutrient levels TOR signaling regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction TORC1 signaling regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization positive regulation of biological process vesicle-mediated transport cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport endocytosis RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis system development morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication postsynaptic modulation of chemical synaptic transmission protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process pattern specification process regionalization dorsal/ventral pattern formation dorsal/ventral neural tube patterning neural tube patterning catabolic process regulation of protein metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of proteasomal protein catabolic process regulation of metabolic process regulation of protein catabolic process formation of primary germ layer mesoderm morphogenesis gastrulation mesoderm formation mesoderm development potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of osteoblast differentiation regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification monosaccharide metabolic process gluconeogenesis positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of gluconeogenesis regulation of biosynthetic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process interleukin-2-mediated signaling pathway cell surface receptor signaling pathway cellular response to interleukin-2 response to cytokine cytokine-mediated signaling pathway response to peptide response to interleukin-2 response to chemical cellular response to cytokine stimulus response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus response to monosaccharide response to carbohydrate response to glucose glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus cellular response to monosaccharide stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound response to glucagon cellular response to glucagon stimulus cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus regulation of steroid biosynthetic process regulation of cholesterol biosynthetic process regulation of cholesterol metabolic process steroid metabolic process regulation of lipid metabolic process sterol metabolic process cholesterol metabolic process lipid biosynthetic process alcohol metabolic process positive regulation of lipid metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process positive regulation of cholesterol biosynthetic process secondary alcohol metabolic process positive regulation of steroid biosynthetic process sterol biosynthetic process positive regulation of lipid biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process regulation of lipid biosynthetic process positive regulation of alcohol biosynthetic process positive regulation of sterol biosynthetic process lipid metabolic process bicellular tight junction assembly regulation of bicellular tight junction assembly tight junction organization apical junction assembly regulation of cellular component biogenesis cellular component biogenesis regulation of cell junction assembly cell junction organization cellular component assembly cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization meiotic cell cycle process involved in oocyte maturation regulation of reproductive process negative regulation of biological process negative regulation of cell cycle female gamete generation regulation of cell development oocyte development cell cycle regulation of meiotic cell cycle regulation of cell cycle process meiotic cell cycle negative regulation of meiotic cell cycle regulation of oocyte maturation meiotic cell cycle process negative regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of cellular process negative regulation of cell differentiation regulation of cell cycle regulation of cell maturation cell cycle process negative regulation of developmental process oogenesis regulation of meiotic cell cycle process involved in oocyte maturation negative regulation of cell cycle process negative regulation of cell development negative regulation of reproductive process oocyte maturation oocyte differentiation negative regulation of cell maturation negative regulation of oocyte maturation negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of protein maturation protein maturation regulation of proteolysis proteolysis regulation of gene expression regulation of protein processing protein processing regulation of macromolecule biosynthetic process regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse secretion by cell signal release spontaneous exocytosis of neurotransmitter neurotransmitter secretion secretion export from cell neurotransmitter transport signal release from synapse exocytosis adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of protein localization positive regulation of nucleocytoplasmic transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport regulation of protein export from nucleus regulation of intracellular transport regulation of establishment of protein localization regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of protein export from nucleus regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport protein localization to organelle protein localization to lipid droplet cAMP/PKA signal transduction intracellular signaling cassette adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway cellular response to parathyroid hormone stimulus response to parathyroid hormone ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration negative regulation of small molecule metabolic process negative regulation of glycolytic process oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process negative regulation of ATP metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process glycolytic process regulation of nucleotide metabolic process pyridine-containing compound metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process negative regulation of metabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process negative regulation of purine nucleotide metabolic process energy derivation by oxidation of organic compounds negative regulation of phosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process negative regulation of nucleotide catabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process regulation of glycolytic process through fructose-6-phosphate ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process negative regulation of glycolytic process through fructose-6-phosphate glycolytic process through fructose-6-phosphate negative regulation of intracellular signal transduction negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling regulation of TORC1 signaling regulation of TOR signaling cellular response to cold response to cold synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of cell communication nitrogen compound transport positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion regulation of hormone secretion regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region peptide secretion regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion positive regulation of peptide secretion regulation of peptide transport positive regulation of protein secretion peptide transport regulation of insulin secretion peptide hormone secretion hormone transport insulin secretion positive regulation of signaling regulation of cellular respiration	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytosol 9+2 motile cilium sperm flagellum motile cilium sperm midpiece synapse cell junction glutamatergic synapse neuromuscular junction perinuclear region of cytoplasm postsynapse acrosomal vesicle intracellular vesicle endomembrane system cytoplasmic vesicle secretory granule secretory vesicle vesicle mitochondrion germinal vesicle germ cell nucleus female germ cell nucleus centrosome microtubule organizing center microtubule cytoskeleton cell periphery plasma membrane membrane presynapse protein-containing complex ciliary base protein kinase complex transferase complex, transferring phosphorus-containing groups catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex cAMP-dependent protein kinase complex serine/threonine protein kinase complex membrane microdomain membrane raft plasma membrane raft plasma membrane region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
B [auth A]	IPR018488	Cyclic nucleotide-binding, conserved site	Conserved Site
B [auth A]	IPR003117	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	Domain
B [auth A]	IPR000595	Cyclic nucleotide-binding domain	Domain
B [auth A]	IPR050503	cAMP-dependent protein kinase regulatory subunit-like	Family
B [auth A]	IPR012198	cAMP-dependent protein kinase regulatory subunit	Family
B [auth A]	IPR018490	Cyclic nucleotide-binding domain superfamily	Homologous Superfamily
A [auth B]	IPR000719	Protein kinase domain	Domain
A [auth B]	IPR044109	cAMP-dependent protein kinase catalytic subunit	Family
A [auth B]	IPR017441	Protein kinase, ATP binding site	Binding Site
A [auth B]	IPR000961	AGC-kinase, C-terminal	Domain
A [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth B]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth A]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A [auth B]	SEP	Parent Component: SER RESID: AA0037 , AA0037 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-serine MOD:00046
A [auth B]	TPO	Parent Component: THR RESID: AA0037 , AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.