4XYM

Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with coenzyme A, Ca-AMPCP and HgCl+

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CoA_binding_2	e4xymA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_2	ECOD (1.6)
A	Ligase_CoA_1	e4xymA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Ligase_CoA_1	ECOD (1.6)
A	Succ_CoA_lig	e4xymA3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Succ_CoA_lig	ECOD (1.6)
C	CoA_binding_2	e4xymC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_2	ECOD (1.6)
C	Ligase_CoA_1	e4xymC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Ligase_CoA_1	ECOD (1.6)
C	Succ_CoA_lig	e4xymC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Succ_CoA_lig	ECOD (1.6)
B	ATP-grasp_2	e4xymB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp_2	ECOD (1.6)
D	ATP-grasp_2	e4xymD1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp_2	ECOD (1.6)

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 (4.3.0)
A	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF19045	Ligase-CoA domain (Ligase_CoA_2)	Ligase-CoA domain	This domain is related to Pfam:PF00549 and adopts a flavodoxin fold [1].	Domain
A, C	PF13380	CoA binding domain (CoA_binding_2)	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, C	PF13607	Succinyl-CoA ligase like flavodoxin domain (Succ_CoA_lig)	Succinyl-CoA ligase like flavodoxin domain	This domain contains the catalytic domain from Succinyl-CoA ligase alpha subunit and other related enzymes. A conserved histidine is involved in phosphoryl transfer.	Domain
B, D	PF13549	ATP-grasp domain (ATP-grasp_5)	ATP-grasp domain	This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	alpha subunit of Acyl-CoA synthetase (NDP forming)	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding acetate-CoA ligase (ADP-forming) activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity	-	-
B, D	beta subunit of Acyl-CoA synthetase (NDP forming)	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR032875	Succinyl-CoA synthetase-like, flavodoxin domain	Domain
A, C	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, C	IPR043938	Ligase-CoA domain	Domain
A, C	IPR016102	Succinyl-CoA synthetase-like	Homologous Superfamily
A, C	IPR003781	CoA-binding	Domain
B, D	IPR011761	ATP-grasp fold	Domain
B, D	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily

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.