3NY5 | pdb_00003ny5

Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo sapiens. Northeast Structural Genomics Consortium Target HR4694F

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3ny5d1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ny5d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ny5c1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ny5c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ny5b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ny5b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ny5a1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ny5a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8071818	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8071818	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8071818	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8071818	3000157	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Cytochrome_CBB3	e3ny5D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
C	Cytochrome_CBB3	e3ny5C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
B	Cytochrome_CBB3	e3ny5B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
A	Rhv	e3ny5A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Rhv	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02196	Raf-like Ras-binding domain (RBD)	Raf-like Ras-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Serine/threonine-protein kinase B-raf	protein serine/threonine kinase activity MAP kinase kinase kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein serine/threonine kinase activity MAP kinase kinase kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding MAP kinase kinase activity protein serine/threonine/tyrosine kinase activity identical protein binding protein binding cation binding calcium ion binding metal ion binding scaffold protein binding protein serine kinase activity transition metal ion binding zinc ion binding	cellular response to stimulus multicellular organismal process regulation of cellular process response to stimulus cell projection organization positive regulation of neuron projection regeneration regulation of cellular response to stress neuron projection development regeneration neuron projection regeneration positive regulation of developmental process multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular response to stimulus multicellular organismal process regulation of cellular process response to stimulus cell projection organization positive regulation of neuron projection regeneration regulation of cellular response to stress neuron projection development regeneration neuron projection regeneration positive regulation of developmental process multicellular organism development neuron differentiation cell differentiation anatomical structure development positive regulation of cell projection organization response to wounding system development positive regulation of response to wounding developmental process regulation of biological process regulation of axon regeneration regulation of cell projection organization response to external stimulus nervous system development generation of neurons regulation of response to stimulus regulation of neuron projection regeneration regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular developmental process regulation of response to external stimulus positive regulation of biological process cell development response to axon injury regulation of response to wounding positive regulation of response to stimulus cellular component organization neurogenesis positive regulation of response to external stimulus cellular response to stress axon regeneration positive regulation of neuron projection development regulation of response to stress response to stress cellular component organization or biogenesis positive regulation of cellular process plasma membrane bounded cell projection organization biological regulation axon development neuron development cellular process positive regulation of axon regeneration regulation of plasma membrane bounded cell projection organization endothelial cell apoptotic process apoptotic process cell death programmed cell death regulation of localization regulated exocytosis synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication CD4-positive or CD8-positive, alpha-beta T cell lineage commitment hemopoiesis cell activation mononuclear cell differentiation T cell lineage commitment lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process positive T cell selection T cell differentiation T cell selection cell fate commitment leukocyte differentiation regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process anatomical structure morphogenesis head development head morphogenesis body morphogenesis cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion positive regulation of nervous system development axonogenesis regulation of cell differentiation regulation of neurogenesis regulation of cell development cell projection morphogenesis neuron projection morphogenesis positive regulation of cell development positive regulation of multicellular organismal process plasma membrane bounded cell projection morphogenesis cell morphogenesis regulation of nervous system development positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development cell morphogenesis involved in neuron differentiation actomyosin structure organization actin cytoskeleton organization actin filament organization cellular component biogenesis organelle organization cellular component assembly actin filament bundle organization contractile actin filament bundle assembly actin filament-based process actin filament bundle assembly stress fiber assembly supramolecular fiber organization cytoskeleton organization positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation phosphate-containing compound metabolic process peptidyl-amino acid modification protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of cell-substrate adhesion regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation regulation of T cell differentiation regulation of immune system process regulation of lymphocyte differentiation regulation of T cell activation regulation of hemopoiesis regulation of lymphocyte activation cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion intracellular signal transduction intracellular signaling cassette MAPK cascade signal transduction T cell differentiation in thymus postsynaptic modulation of chemical synaptic transmission cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway ERBB signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway somatic stem cell population maintenance maintenance of cell number stem cell population maintenance cellular response to xenobiotic stimulus response to xenobiotic stimulus negative regulation of locomotion regulation of cell motility regulation of fibroblast migration fibroblast migration negative regulation of fibroblast migration regulation of locomotion ameboidal-type cell migration regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion face development immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response positive regulation of immune system process immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response immune system development animal organ development gland development hematopoietic or lymphoid organ development thymus development animal organ morphogenesis positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling thyroid gland development endocrine system development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process response to light stimulus system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning behavior response to radiation response to abiotic stimulus neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process myeloid progenitor cell differentiation hematopoietic progenitor cell differentiation cell population proliferation regulation of cell population proliferation establishment of protein localization establishment of protein localization to membrane localization within membrane negative regulation of endothelial cell apoptotic process regulation of endothelial cell apoptotic process CD4-positive, alpha-beta T cell differentiation alpha-beta T cell differentiation CD4-positive, alpha-beta T cell activation alpha-beta T cell activation hexose transmembrane transport carbohydrate transport positive regulation of D-glucose transmembrane transport transmembrane transport regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport long-term synaptic potentiation regulation of biological quality regulation of synaptic plasticity positive regulation of synaptic transmission positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly positive regulation of stress fiber assembly regulation of actin filament organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization regulation of supramolecular fiber organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece synapse cell junction glutamatergic synapse neuron projection cell body postsynapse intracellular membraneless organelle intracellular organelle ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton mitochondrion intracellular membrane-bounded organelle sperm end piece centrosome centriolar satellite cell periphery plasma membrane membrane presynapse nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003116	Raf-like Ras-binding	Domain
A, B, C, D	IPR020454	Diacylglycerol/phorbol-ester binding	Domain
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR051681	Serine/Threonine Kinases and Pseudokinases	Family
A, B, C, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR046349	C1-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P15056	cardiofaciocutaneous syndrome Noonan syndrome Noonan syndrome with multiple lentigines malignant glioma colorectal cancer Noonan syndrome 7 gastrointestinal stromal tumor Costello syndrome Erdheim-Chester disease melanoma craniopharyngioma pilocytic astrocytoma ameloblastoma cancer hairy cell leukemia cardiofaciocutaneous syndrome Noonan syndrome Noonan syndrome with multiple lentigines malignant glioma colorectal cancer Noonan syndrome 7 gastrointestinal stromal tumor Costello syndrome Erdheim-Chester disease melanoma craniopharyngioma pilocytic astrocytoma ameloblastoma cancer hairy cell leukemia adrenal cortex carcinoma subependymal giant cell astrocytoma LEOPARD syndrome 3 lung cancer astrocytic tumor cardiomyopathy hepatocellular carcinoma protoplasmic astrocytoma mixed glioma Neoplasms, Experimental fibrillary astrocytoma childhood cerebral astrocytoma plasma cell myeloma intellectual disability adamantinous craniopharyngioma prostate cancer juvenile pilocytic astrocytoma Sezary syndrome Langerhans cell histiocytosis anaplastic astrocytoma cutaneous melanoma neuroendocrine neoplasm thyroid gland carcinoma cardiofaciocutaneous syndrome 1 gemistocytic astrocytoma Hashimoto-Pritzker syndrome cholangiocarcinoma papillary craniopharyngioma primary cutaneous T-cell non-Hodgkin lymphoma thyroid adenoma liver cancer Noonan syndrome 1 gastric neoplasm oligodendroglioma glioblastoma granulomatous slack skin disease childhood brain stem glioma ovarian carcinoma chronic myelogenous leukemia, BCR-ABL1 positive hypertrophic cardiomyopathy adamantinoma mandibular cancer prostate adenocarcinoma adrenal carcinoma congenital anemia kidney neoplasm stomach carcinoma in situ large congenital melanocytic nevus astrocytoma (excluding glioblastoma) thyroid cancer benign neoplasm of stomach lung benign neoplasm breast adenocarcinoma non-Hodgkin lymphoma nongerminomatous germ cell tumor type 2 diabetes mellitus malignant colon neoplasm cerebral astrocytoma osteosarcoma glioma ovarian neoplasm histiocytosis colon carcinoma colorectal carcinoma psoriasis atypical teratoid rhabdoid tumor thyroid cancer, nonmedullary, 1 liver neoplasm breast carcinoma non-Langerhans cell histiocytosis familial nonmedullary thyroid carcinoma tuberculosis lymphoma, non-Hodgkin, familial gastric carcinoma malignant ependymoma Charcot-Marie-Tooth disease ovarian cancer hydrops fetalis colorectal adenocarcinoma interstitial cystitis kidney cancer renal cell carcinoma spina bifida large cell medulloblastoma cystadenoma B-cell chronic lymphocytic leukemia diffuse astrocytoma thyroid cancer, nonmedullary, 2 lung adenocarcinoma neurofibromatosis type 1 exocrine pancreatic carcinoma thyroid gland papillary carcinoma lung carcinoma non-small cell lung carcinoma

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.