6ECF

Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hydrolase_4_1	e6ecfA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
B	Hydrolase_4_1	e6ecfB1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
C	Hydrolase_4_1	e6ecfC1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
D	Hydrolase_4_1	e6ecfD1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
E	Hydrolase_4_1	e6ecfE1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
F	Hydrolase_4_1	e6ecfF1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00975	Thioesterase domain (Thioesterase)	Thioesterase domain	Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of v ...	Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa.	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	Vlm2	vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding catalytic activity	organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process secondary metabolite biosynthetic process secondary metabolic process amide biosynthetic process amide metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process secondary metabolite biosynthetic process secondary metabolic process amide biosynthetic process amide metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process small molecule metabolic process cellular process organic acid metabolic process	-
G, H [auth I], I [auth H], J [auth K], K [auth J], G, H [auth I], I [auth H], J [auth K], K [auth J], L	dodecadepsipeptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006162	Phosphopantetheine attachment site	PTM
A, B, C, D, E A, B, C, D, E, F	IPR020845	AMP-binding, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013968	Polyketide synthase, ketoreductase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001242	Condensation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036736	ACP-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009081	Phosphopantetheine binding ACP domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR010071	Amino acid adenylation domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR020802	Polyketide synthase, thioesterase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR042099	ANL, N-terminal domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001031	Thioesterase	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	DPP	Parent Component: ALA
G, H [auth I], I [auth H], J [auth K], K [auth J], G, H [auth I], I [auth H], J [auth K], K [auth J], L	2OP
G, H [auth I], I [auth H], J [auth K], K [auth J], G, H [auth I], I [auth H], J [auth K], K [auth J], L	DVA	RESID: AA0200 PSI-MOD : D-valine MOD:00705
G, H [auth I], I [auth H], J [auth K], K [auth J], G, H [auth I], I [auth H], J [auth K], K [auth J], L	VAD	Parent Component: VAL RESID: AA0200

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.