6ECF | pdb_00006ecf

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

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
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)
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)
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)
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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-	-	-
A, B, C, D, E A, B, C, D, E, F	Vlm2	vitamin binding modified amino acid binding binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding catalytic activity	secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process nonribosomal peptide biosynthetic process peptide metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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	IPR057326	Ketoreductase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR045851	AMP-binding enzyme domain superfamily	Homologous Superfamily
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	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	IPR020802	Thioesterase TesA-like	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	IPR020806	Polyketide synthase-like, phosphopantetheine-binding 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	IPR013968	Polyketide synthase-like, ketoreductase domain	Domain
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
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
A, B, C, D, E A, B, C, D, E, F	DPP	Parent Component: ALA RESID: AA0200

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.