6WCV | pdb_00006wcv

Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6wcva1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	CoA-binding domain	Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6wcva2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, alpha-chain, C-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6wcva3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6wcvb2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, beta-chain, C-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6wcvb1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Succinyl-CoA synthetase, beta-chain, N-terminal domain	Succinyl-CoA synthetase, beta-chain, N-terminal domain	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)
A	MCM_N	e6wcvA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: MCM_N	ECOD (v294.1)
B	MCM_N	e6wcvB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: MCM_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
A	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (utative)
B	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02629	CoA binding domain (CoA_binding)	CoA binding domain	This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.	Domain
A	PF00549	CoA-ligase (Ligase_CoA)	CoA-ligase	This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP.	Domain
B	PF08442	ATP-grasp domain (ATP-grasp_2)	ATP-grasp domain		Domain
B	PF00549	CoA-ligase (Ligase_CoA)	CoA-ligase	This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	succinate-CoA ligase (ADP-forming) activity succinate-CoA ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding succinate-CoA ligase (GDP-forming) activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process catabolic process organophosphate catabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process catabolic process organophosphate catabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process succinyl-CoA catabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process sulfur compound metabolic process succinyl-CoA metabolic process phosphorus metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle succinate-CoA ligase complex (ADP-forming) protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex succinate-CoA ligase complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle succinate-CoA ligase complex (ADP-forming) protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex succinate-CoA ligase complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen succinate-CoA ligase complex (GDP-forming)
B	Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding GDP binding guanyl ribonucleotide binding protein-containing complex binding GTP binding succinate-CoA ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity succinate-CoA ligase (GDP-forming) activity acid-thiol ligase activity ligase activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process succinyl-CoA metabolic process phosphorus metabolic process succinate metabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process catabolic process organophosphate catabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process succinyl-CoA catabolic process sulfur compound catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex succinate-CoA ligase complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen succinate-CoA ligase complex (GDP-forming)

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016102	Succinyl-CoA synthetase-like	Homologous Superfamily
A	IPR017440	ATP-citrate lyase/succinyl-CoA ligase, active site	Active Site
A	IPR033847	ATP-citrate lyase/succinyl-CoA ligase, conserved site	Conserved Site
A	IPR003781	CoA-binding	Domain
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR005810	Succinyl-CoA ligase, alpha subunit	Family
A	IPR005811	ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain	Domain
B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
B	IPR016102	Succinyl-CoA synthetase-like	Homologous Superfamily
B	IPR013650	ATP-grasp fold, succinyl-CoA synthetase-type	Domain
B	IPR017866	Succinyl-CoA synthetase, beta subunit, conserved site	Conserved Site
B	IPR034722	Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial	Family
B	IPR005811	ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain	Domain
B	IPR005809	Succinate--CoA ligase-like, beta subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P53597	mitochondrial DNA depletion syndrome 9 Disease Exacerbation gastric cancer osteosarcoma plasma cell myeloma gastric neoplasm intellectual disability ovarian cancer ulcerative colitis hereditary diffuse gastric adenocarcinoma Leigh syndrome mitochondrial DNA depletion syndrome mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria pancreatic ductal adenocarcinoma
B	Pharos: Q96I99	methylmalonic acidemia endometriosis lung adenocarcinoma obesity disorder pilocytic astrocytoma subependymal giant cell astrocytoma Adenocarcinoma of Lung lung cancer malignant mesothelioma ovarian cancer plasma cell myeloma tuberculosis astrocytic tumor Down syndrome glioblastoma methylmalonic acidemia endometriosis lung adenocarcinoma obesity disorder pilocytic astrocytoma subependymal giant cell astrocytoma Adenocarcinoma of Lung lung cancer malignant mesothelioma ovarian cancer plasma cell myeloma tuberculosis astrocytic tumor Down syndrome glioblastoma lymphoplasmacytic lymphoma MALT lymphoma pancreatic ductal adenocarcinoma psoriasis ulcerative colitis breast cancer malignant colon neoplasm medulloblastoma

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.