5VG7 | pdb_00005vg7

Crystal Structure of the R503Q missense variant of human PGM1

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5vg7b1	Alpha and beta proteins (a/b)	Phosphoglucomutase, first 3 domains	Phosphoglucomutase, first 3 domains	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vg7b4	Alpha and beta proteins (a+b)	TBP-like	Phosphoglucomutase, C-terminal domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vg7b5	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vg7a1	Alpha and beta proteins (a/b)	Phosphoglucomutase, first 3 domains	Phosphoglucomutase, first 3 domains	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vg7a4	Alpha and beta proteins (a+b)	TBP-like	Phosphoglucomutase, C-terminal domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5vg7a5	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	Chlorophyllase2	e5vg7B1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
A	bZIP_1	e5vg7A1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: bZIP_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate	Chain A, domain 3	CATH (4.3.0)
B	3.30.310.50	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Alpha-D-phosphohexomutase, C-terminal domain	CATH (4.3.0)
A	3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate	Chain A, domain 3	CATH (4.3.0)
A	3.30.310.50	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Alpha-D-phosphohexomutase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02878	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I (PGM_PMM_I)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I		Domain
B	PF02879	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II (PGM_PMM_II)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II		Domain
B	PF02880	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III (PGM_PMM_III)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III		Domain
B	PF24947	Phosphoglucomutase-1, C-terminal domain (PGM1_C_vert_fung)	Phosphoglucomutase-1, C-terminal domain	This entry represents the C-terminal domain of phosphoglucomutase-1 (PGM1) from human, and its homologues from vertebrates and fungi, which catalyses the bi-directional interconversion between alpha-D-glucose 1-phosphate (G1P) and alpha-D-glucose 6-p ...	This entry represents the C-terminal domain of phosphoglucomutase-1 (PGM1) from human, and its homologues from vertebrates and fungi, which catalyses the bi-directional interconversion between alpha-D-glucose 1-phosphate (G1P) and alpha-D-glucose 6-phosphate (G6P), a reaction that is essential for normal carbohydrate metabolism and is also important in the cytoplasmic biosynthesis of nucleotide sugars needed for glycan biosynthesis [2-5]. This domain contains a six-stranded antiparallel beta-sheet with two alpha-helices lying on the face of the sheet opposite the active site which is located centrally, in a deep cleft between the four domains of these proteins [1-5]. This domain contains the phosphate-binding loop which interacts with the substrate phosphate moiety [5].	Domain
A	PF02878	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I (PGM_PMM_I)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I		Domain
A	PF02879	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II (PGM_PMM_II)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II		Domain
A	PF02880	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III (PGM_PMM_III)	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III		Domain
A	PF24947	Phosphoglucomutase-1, C-terminal domain (PGM1_C_vert_fung)	Phosphoglucomutase-1, C-terminal domain	This entry represents the C-terminal domain of phosphoglucomutase-1 (PGM1) from human, and its homologues from vertebrates and fungi, which catalyses the bi-directional interconversion between alpha-D-glucose 1-phosphate (G1P) and alpha-D-glucose 6-p ...	This entry represents the C-terminal domain of phosphoglucomutase-1 (PGM1) from human, and its homologues from vertebrates and fungi, which catalyses the bi-directional interconversion between alpha-D-glucose 1-phosphate (G1P) and alpha-D-glucose 6-phosphate (G6P), a reaction that is essential for normal carbohydrate metabolism and is also important in the cytoplasmic biosynthesis of nucleotide sugars needed for glycan biosynthesis [2-5]. This domain contains a six-stranded antiparallel beta-sheet with two alpha-helices lying on the face of the sheet opposite the active site which is located centrally, in a deep cleft between the four domains of these proteins [1-5]. This domain contains the phosphate-binding loop which interacts with the substrate phosphate moiety [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Phosphoglucomutase-1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoglucomutase activity isomerase activity intramolecular phosphotransferase activity catalytic activity intramolecular transferase activity	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration 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 ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration 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 nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate 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 cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds 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 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 hexose catabolic process galactose catabolic process galactose metabolic process galactose catabolic process via UDP-galactose, Leloir pathway monosaccharide catabolic process small molecule catabolic process glucan catabolic process glycogen metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process polysaccharide catabolic process energy reserve metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle cytosol ficolin-1-rich granule ficolin-1-rich granule lumen
A	Phosphoglucomutase-1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoglucomutase activity isomerase activity intramolecular phosphotransferase activity catalytic activity intramolecular transferase activity	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration 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 ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration 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 nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate 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 cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds 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 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 hexose catabolic process galactose catabolic process galactose metabolic process galactose catabolic process via UDP-galactose, Leloir pathway monosaccharide catabolic process small molecule catabolic process glucan catabolic process glycogen metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process polysaccharide catabolic process energy reserve metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure tertiary granule lumen membrane-enclosed lumen intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen tertiary granule intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle cytosol ficolin-1-rich granule ficolin-1-rich granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR045244	Phosphoglucomutase	Family
B	IPR005846	Alpha-D-phosphohexomutase, alpha/beta/alpha domain III	Domain
B	IPR005845	Alpha-D-phosphohexomutase, alpha/beta/alpha domain II	Domain
B	IPR016055	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III	Homologous Superfamily
B	IPR016066	Alpha-D-phosphohexomutase, conserved site	Conserved Site
B	IPR005844	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I	Domain
B	IPR005841	Alpha-D-phosphohexomutase superfamily	Family
B	IPR036900	Alpha-D-phosphohexomutase, C-terminal domain superfamily	Homologous Superfamily
A	IPR045244	Phosphoglucomutase	Family
A	IPR005846	Alpha-D-phosphohexomutase, alpha/beta/alpha domain III	Domain
A	IPR005845	Alpha-D-phosphohexomutase, alpha/beta/alpha domain II	Domain
A	IPR016055	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III	Homologous Superfamily
A	IPR016066	Alpha-D-phosphohexomutase, conserved site	Conserved Site
A	IPR005844	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I	Domain
A	IPR005841	Alpha-D-phosphohexomutase superfamily	Family
A	IPR036900	Alpha-D-phosphohexomutase, C-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P36871	PGM1-CDG congenital disorder of glycosylation glycogen storage disease colorectal cancer ovarian cancer plasma cell myeloma breast cancer colorectal carcinoma coronary artery disease ductal breast carcinoma in situ intellectual disability large cell medulloblastoma medulloblastoma pancreatic ductal adenocarcinoma rhabdomyolysis PGM1-CDG congenital disorder of glycosylation glycogen storage disease colorectal cancer ovarian cancer plasma cell myeloma breast cancer colorectal carcinoma coronary artery disease ductal breast carcinoma in situ intellectual disability large cell medulloblastoma medulloblastoma pancreatic ductal adenocarcinoma rhabdomyolysis breast carcinoma Colorectal Neoplasms cystic fibrosis invasive ductal breast carcinoma lymphoplasmacytic lymphoma myocardial ischemia drug-induced liver injury inborn errors of metabolism malignant mesothelioma
A	Pharos: P36871	PGM1-CDG congenital disorder of glycosylation glycogen storage disease colorectal cancer ovarian cancer plasma cell myeloma breast cancer colorectal carcinoma coronary artery disease ductal breast carcinoma in situ intellectual disability large cell medulloblastoma medulloblastoma pancreatic ductal adenocarcinoma rhabdomyolysis PGM1-CDG congenital disorder of glycosylation glycogen storage disease colorectal cancer ovarian cancer plasma cell myeloma breast cancer colorectal carcinoma coronary artery disease ductal breast carcinoma in situ intellectual disability large cell medulloblastoma medulloblastoma pancreatic ductal adenocarcinoma rhabdomyolysis breast carcinoma Colorectal Neoplasms cystic fibrosis invasive ductal breast carcinoma lymphoplasmacytic lymphoma myocardial ischemia drug-induced liver injury inborn errors of metabolism malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.