3C39

Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate

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)
A	d3c39a_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3c39b_	Alpha and beta proteins (a/b)	Phosphoglycerate kinase	Phosphoglycerate kinase	Phosphoglycerate kinase	automated matches	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)
A	SCOP2B Superfamily	Phosphoglycerate kinase	8069301	3001564	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoglycerate kinase	8069301	3001564	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)
A	PGK_N	e3c39A1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
A	PGK_C	e3c39A2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)
B	PGK_N	e3c39B1	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 1 (From Topology)	H: Phosphoglycerate kinase domain 1 (From Topology)	T: Phosphoglycerate kinase domain 1	F: PGK_N	ECOD (1.6)
B	PGK_C	e3c39B2	A: a/b three-layered sandwiches	X: Phosphoglycerate kinase domain 2 (From Topology)	H: Phosphoglycerate kinase domain 2 (From Topology)	T: Phosphoglycerate kinase domain 2	F: PGK_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)
B	3.40.50.1260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate kinase, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00162	Phosphoglycerate kinase (PGK)	Phosphoglycerate kinase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphoglycerate kinase 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ADP binding oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity protein-disulfide reductase (NAD(P)H) activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor phosphoglycerate kinase activity kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity transferase activity, transferring phosphorus-containing groups	ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process cellular metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process catabolic process ATP 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 ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process purine ribonucleoside diphosphate catabolic process monosaccharide metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process biosynthetic process glucose metabolic process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus phosphorylation multicellular organismal process regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of biological process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis biological regulation vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process NADH regeneration glucose catabolic process to pyruvate hexose catabolic process NADH metabolic process glucose catabolic process monosaccharide catabolic process small molecule catabolic process canonical glycolysis NAD metabolic process glycolytic process through glucose-6-phosphate NAD catabolic process glycolytic process through fructose-6-phosphate epithelium development cellular developmental process cell differentiation tissue development epithelial cell differentiation zymogen activation cellular biosynthetic process gene expression macromolecule biosynthetic process protein maturation proteolysis protein processing protein metabolic process macromolecule metabolic process plasminogen activation	membrane cellular anatomical entity 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 cellular anatomical entity 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 microdomain membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036043	Phosphoglycerate kinase superfamily	Homologous Superfamily
A, B	IPR001576	Phosphoglycerate kinase	Family
A, B	IPR015824	Phosphoglycerate kinase, N-terminal	Homologous Superfamily
A, B	IPR015911	Phosphoglycerate kinase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P00558	glycogen storage disease due to phosphoglycerate kinase 1 deficiency renal cell carcinoma papillary renal cell carcinoma collecting duct carcinoma familial hemolytic anemia chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma Liver carcinoma malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma adrenal cortex carcinoma breast carcinoma plasma cell myeloma hemolytic anemia glycogen storage disease due to phosphoglycerate kinase 1 deficiency renal cell carcinoma papillary renal cell carcinoma collecting duct carcinoma familial hemolytic anemia chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma Liver carcinoma malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma adrenal cortex carcinoma breast carcinoma plasma cell myeloma hemolytic anemia invasive ductal breast carcinoma lung adenocarcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor psoriasis rhabdomyolysis dermatomyositis glioblastoma hepatocellular carcinoma lymphoplasmacytic lymphoma myopathy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm breast cancer Pick disease clear cell renal carcinoma renal carcinoma cystic fibrosis ductal breast carcinoma in situ intellectual disability

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.