1YJX

Crystal structure of human B type phosphoglycerate mutase

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	d1yjxa_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1yjxb_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1yjxc_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1yjxf_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1yjxg_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1yjxh_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d1yjxi_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d1yjxk_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1yjxd_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1yjxe_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d1yjxj_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d1yjxl_	Alpha and beta proteins (a/b)	Phosphoglycerate mutase-like	Phosphoglycerate mutase-like	Cofactor-dependent phosphoglycerate mutase	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	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Histidine phosphatase-like	8070063	3000781	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	His_Phos_1	e1yjxA1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
B	His_Phos_1	e1yjxB1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
C	His_Phos_1	e1yjxC1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
F	His_Phos_1	e1yjxF1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
G	His_Phos_1	e1yjxG1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
H	His_Phos_1	e1yjxH1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
I	His_Phos_1	e1yjxI1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
K	His_Phos_1	e1yjxK1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
D	His_Phos_1	e1yjxD1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
E	His_Phos_1	e1yjxE1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
J	His_Phos_1	e1yjxJ1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)
L	His_Phos_1	e1yjxL1	A: a/b three-layered sandwiches	X: Phosphoglycerate mutase-like (From Topology)	H: Phosphoglycerate mutase-like (From Topology)	T: Phosphoglycerate mutase-like	F: His_Phos_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
B	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
C	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
F	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
G	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
H	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
I	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
K	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
D	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
E	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
J	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)
L	3.40.50.1240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphoglycerate mutase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF00300	Histidine phosphatase superfamily (branch 1) (His_Phos_1)	Histidine phosphatase superfamily (branch 1)	The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the p ...	The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Phosphoglycerate mutase 1	protein binding binding kinase binding enzyme binding protein kinase binding hydrolase activity catalytic activity bisphosphoglycerate mutase activity isomerase activity intramolecular phosphotransferase activity intramolecular transferase activity 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity phosphoglycerate mutase activity	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 organonitrogen compound catabolic 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 organic cyclic compound metabolic 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 organic substance 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 organonitrogen compound metabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy organic cyclic compound catabolic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process organic substance catabolic 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 organic substance biosynthetic process glucose metabolic process respiratory burst regulation of amide metabolic process regulation of cellular process regulation of generation of precursor metabolites and energy regulation of primary metabolic process regulation of small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process regulation of pentose-phosphate shunt pentose-phosphate shunt regulation of nucleobase-containing compound metabolic process regulation of carbohydrate catabolic process regulation of biological process regulation of cellular metabolic process regulation of purine nucleotide metabolic process regulation of phosphorus metabolic process regulation of metabolic process glucose 6-phosphate metabolic process regulation of NADP metabolic process amide metabolic process regulation of carbohydrate metabolic process biological regulation regulation of catabolic process NADP metabolic process NADPH regeneration 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 regulation of ATP metabolic process regulation of purine nucleotide catabolic process regulation of nucleotide catabolic process regulation of glycolytic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen secretory granule secretory vesicle cytoplasm cytosol ficolin-1-rich granule ficolin-1-rich granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR013078	Histidine phosphatase superfamily, clade-1	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001345	Phosphoglycerate/bisphosphoglycerate mutase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029033	Histidine phosphatase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR005952	Phosphoglycerate mutase 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Pharos: P18669	squamous cell carcinoma non-small cell lung carcinoma adenocarcinoma carcinoma granular cell carcinoma Mammary Neoplasms, Experimental tubular adenocarcinoma sarcomatoid carcinoma cribriform carcinoma of breast oral cavity neoplasm gastric cancer hereditary diffuse gastric adenocarcinoma undifferentiated carcinoma bipolar disorder cribriform carcinoma squamous cell carcinoma non-small cell lung carcinoma adenocarcinoma carcinoma granular cell carcinoma Mammary Neoplasms, Experimental tubular adenocarcinoma sarcomatoid carcinoma cribriform carcinoma of breast oral cavity neoplasm gastric cancer hereditary diffuse gastric adenocarcinoma undifferentiated carcinoma bipolar disorder cribriform carcinoma gastric neoplasm mammary neoplasms, animal

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.