4WNC | pdb_00004wnc

Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	SCOP2B (2022-06-29)
A [auth O]	SCOP2B Superfamily	GAPDH-like	8044622	3000043	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)
C [auth B]	2OG-FeII_Oxy_4	e4wncB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
G [auth F]	2OG-FeII_Oxy_4	e4wncF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
H [auth G]	2OG-FeII_Oxy_4	e4wncG1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
F [auth E]	2OG-FeII_Oxy_4	e4wncE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
E [auth D]	2OG-FeII_Oxy_4	e4wncD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
D [auth C]	2OG-FeII_Oxy_4	e4wncC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
B [auth A]	2OG-FeII_Oxy_4	e4wncA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)
A [auth O]	2OG-FeII_Oxy_4	e4wncO1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: 2OG-FeII_Oxy_4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth B]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
G [auth F]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G [auth F]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
H [auth G]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H [auth G]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F [auth E]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F [auth E]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
E [auth D]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E [auth D]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth C]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B [auth A]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth A]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A [auth O]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth O]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain (Gp_dh_C)	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.	Domain
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain (Gp_dh_N)	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain	GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	Glyceraldehyde-3-phosphate dehydrogenase	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding transferase activity, transferring nitrogenous groups catalytic activity, acting on a protein cytoskeletal protein binding microtubule binding protein binding binding tubulin binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding transferase activity, transferring nitrogenous groups catalytic activity, acting on a protein peptidyl-cysteine S-nitrosylase activity transferase activity catalytic activity enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity aspartic-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor NAD binding disordered domain specific binding protein domain specific binding identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein stability regulation of biological quality protein stabilization catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy process utilizing autophagic mechanism 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 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 monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration 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 purine ribonucleoside diphosphate catabolic process negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of catalytic activity negative regulation of endopeptidase activity negative regulation of peptidase activity regulation of proteolysis proteolysis regulation of endopeptidase activity regulation of peptidase activity negative regulation of molecular function regulation of molecular function regulation of hydrolase activity biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus peptidyl-cysteine modification peptidyl-cysteine S-nitrosylation peptidyl-cysteine S-trans-nitrosylation macromolecule modification peptidyl-amino acid modification protein modification process protein nitrosylation neuron apoptotic process apoptotic process cell death programmed cell death humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide defense response to fungus response to fungus cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production glucose catabolic process to pyruvate hexose catabolic process hexose metabolic process glucose catabolic process monosaccharide catabolic process small molecule catabolic process monosaccharide metabolic process canonical glycolysis glycolytic process through glucose-6-phosphate glycolytic process through fructose-6-phosphate glucose metabolic process positive regulation of type I interferon production type I interferon production regulation of type I interferon production	cellular anatomical structure membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane cellular anatomical structure membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytoplasm cytosol protein-containing complex GAIT complex cell periphery plasma membrane cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton lipid droplet perinuclear region of cytoplasm ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], A [auth O], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	Pharos: P04406	squamous cell carcinoma acute coronary syndrome Hypoxia colorectal cancer osteoporosis esophageal cancer lung adenocarcinoma ovarian disease eye disease hematologic disease urinary bladder disease lung cancer lymphoplasmacytic lymphoma atherosclerosis neurodegenerative disease squamous cell carcinoma acute coronary syndrome Hypoxia colorectal cancer osteoporosis esophageal cancer lung adenocarcinoma ovarian disease eye disease hematologic disease urinary bladder disease lung cancer lymphoplasmacytic lymphoma atherosclerosis neurodegenerative disease cancer oral cavity neoplasm colonic disease pancreatic ductal adenocarcinoma glioblastoma hepatocellular carcinoma prostate disease stomach disease liver disease uterine disease lung disease autoimmune disease non-small cell lung carcinoma cerebrovascular disorder osteoarthritis coronary artery disease ovarian cancer plasma cell myeloma heart disease hypertensive disorder skin disease kidney disease type 2 diabetes mellitus vertebral column disease lymphatic system disease malignant pancreatic neoplasm arthritic joint disease neoplasm of esophagus breast disease obesity disorder osteoarthritis susceptibility 1 colorectal carcinoma

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.