3LDP | pdb_00003ldp

Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with small molecule inhibitor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d3ldpb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ldpa1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3ldpB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: AAA	F:	ECOD (20:10:01)
A		e3ldpA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: AAA	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.30.30	Alpha Beta	2-Layer Sandwich	Defensin A-like		CATH (4.3.0)
B	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.30.30	Alpha Beta	2-Layer Sandwich	Defensin A-like		CATH (4.3.0)
A	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00012	Hsp70 protein (HSP70)	Hsp70 protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	78 kDa glucose-regulated protein	protein binding binding misfolded protein binding heat shock protein binding protein-folding chaperone 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 protein binding binding misfolded protein binding heat shock protein binding protein-folding chaperone 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 cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding calcium ion binding metal ion binding protein domain specific binding molecular sequestering activity protein sequestering activity ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity unfolded protein binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus regulation of cellular process response to stimulus protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus regulation of cellular process response to stimulus signaling regulation of cellular response to stress endoplasmic reticulum unfolded protein response regulation of response to endoplasmic reticulum stress regulation of signal transduction intracellular signal transduction cell communication regulation of endoplasmic reticulum unfolded protein response cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress signal transduction regulation of IRE1-mediated unfolded protein response response to endoplasmic reticulum stress regulation of biological process regulation of signaling cellular response to topologically incorrect protein biological regulation cellular response to unfolded protein response to unfolded protein regulation of response to stimulus response to topologically incorrect protein IRE1-mediated unfolded protein response regulation of cell communication catabolic process proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway response to chemical cellular response to nutrient levels response to nutrient levels response to starvation cellular response to glucose starvation cellular response to starvation response to interleukin-4 response to peptide response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 ATF6-mediated unfolded protein response regulation of ATF6-mediated unfolded protein response ER-nucleus signaling pathway regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly negative regulation of cellular process cellular component organization or biogenesis developmental process multicellular organismal process head development animal organ development brain development nervous system development cerebellar cortex development multicellular organism development cerebellar Purkinje cell layer development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development cerebellum morphogenesis hindbrain morphogenesis anatomical structure morphogenesis cerebellum structural organization anatomical structure arrangement hindbrain structural organization negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus negative regulation of signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of intracellular signal transduction negative regulation of IRE1-mediated unfolded protein response negative regulation of endoplasmic reticulum unfolded protein response negative regulation of response to endoplasmic reticulum stress maintenance of protein location cellular localization maintenance of location maintenance of location in cell localization maintenance of protein localization in endoplasmic reticulum maintenance of protein location in cell macromolecule localization protein localization to organelle maintenance of protein localization in organelle intracellular protein localization protein localization to endoplasmic reticulum response to biotic stimulus cellular response to biotic stimulus ER overload response positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process establishment of protein localization transport protein targeting protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport intracellular protein transport protein targeting to ER negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of protein folding in endoplasmic reticulum regulation of protein folding protein folding in endoplasmic reticulum regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal substantia nigra development midbrain development neural nucleus development positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion PERK-mediated unfolded protein response integrated stress response signaling intracellular signaling cassette regulation of PERK-mediated unfolded protein response negative regulation of PERK-mediated unfolded protein response	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum endoplasmic reticulum-Golgi intermediate compartment mitochondrion midbody anchoring junction cell junction focal adhesion cell-substrate junction pigment granule intracellular vesicle melanosome cytoplasmic vesicle cell surface cell periphery plasma membrane protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane endoplasmic reticulum chaperone complex endoplasmic reticulum protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR042050	Endoplasmic reticulum chaperone BIP, nucleotide-binding domain	Domain
A, B	IPR013126	Heat shock protein 70 family	Family
A, B	IPR018181	Heat shock protein 70, conserved site	Conserved Site
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P11021	spinocerebellar ataxia type 17 asbestosis chronic myelogenous leukemia, BCR-ABL1 positive esophageal squamous cell carcinoma obesity disorder Respiratory Hypersensitivity myocardial infarction hematopoietic and lymphoid system neoplasm ovarian cancer bipolar I disorder hepatocellular carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma tuberculosis astrocytic tumor spinocerebellar ataxia type 17 asbestosis chronic myelogenous leukemia, BCR-ABL1 positive esophageal squamous cell carcinoma obesity disorder Respiratory Hypersensitivity myocardial infarction hematopoietic and lymphoid system neoplasm ovarian cancer bipolar I disorder hepatocellular carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma tuberculosis astrocytic tumor breast cancer Crohn disease glioblastoma osteosarcoma plasma cell myeloma Sjogren syndrome bipolar disorder cancer drug-induced liver injury lung adenocarcinoma myopathy

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.