5M6Z | pdb_00005m6z

The X-ray structure of human M189I PGK-1 mutant in partially closed conformation

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	d5m6za_	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SH3_2	e5m6zA1	A: alpha bundles	X: SH3	H: SH3	T: SH3	F: SH3_2	ECOD (develop294)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Phosphoglycerate kinase 1	phosphoglycerate kinase activity kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor protein kinase activity phosphoglycerate kinase activity kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor 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 ADP binding protein binding transmembrane transporter binding protein serine/threonine kinase activity cation binding metal ion binding	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 cellular 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 cellular process aerobic respiration regulation of acyl-CoA biosynthetic process negative regulation of small molecule metabolic process regulation of cellular process oxoacid metabolic process regulation of lipid metabolic process negative regulation of biological process acetyl-CoA metabolic process organic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process sulfur compound metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process regulation of biological process negative regulation of metabolic process pyruvate decarboxylation to acetyl-CoA primary metabolic process regulation of ketone metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of fatty acid metabolic process metabolic process regulation of phosphorus metabolic process monocarboxylic acid metabolic process regulation of metabolic process cellular respiration energy derivation by oxidation of organic compounds ketone metabolic process negative regulation of phosphate metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process negative regulation of cellular process negative regulation of pyruvate decarboxylation to acetyl-CoA regulation of pyruvate decarboxylation to acetyl-CoA regulation of biosynthetic process fatty acid metabolic process biological regulation carboxylic acid metabolic process generation of precursor metabolites and energy nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process negative regulation of biosynthetic process negative regulation of phosphorus metabolic process lipid metabolic process developmental process epithelium development cellular developmental process cell differentiation anatomical structure development tissue development epithelial cell differentiation zymogen activation gene expression macromolecule biosynthetic process protein maturation proteolysis protein processing protein metabolic process macromolecule metabolic process plasminogen activation ribonucleotide catabolic process pyridine nucleotide catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process glycolytic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process nicotinamide nucleotide metabolic process purine nucleoside diphosphate 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 nucleoside triphosphate 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 purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process ADP metabolic process purine ribonucleoside diphosphate metabolic 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 glucose metabolic process multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development 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 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 glucose catabolic process to pyruvate hexose catabolic process glucose catabolic process monosaccharide catabolic process small molecule catabolic process canonical glycolysis glycolytic process through glucose-6-phosphate glycolytic process through fructose-6-phosphate	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 microdomain membrane raft mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.