4ZXI

Crystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and Glycine

External Resource: Annotation

Domain Annotation: ECOD Classification
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	AMP-binding_3rd	e4zxiA1	A: beta barrels	X: beta-barrel domain in acetyl-CoA synthetase-like proteins (From Topology)	H: beta-barrel domain in acetyl-CoA synthetase-like proteins (From Topology)	T: beta-barrel domain in acetyl-CoA synthetase-like proteins	F: AMP-binding_3rd	ECOD (1.6)
A	PP-binding	e4zxiA5	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
A	AMP-binding_C	e4zxiA2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: a+b domain in acetyl-CoA synthetase-like proteins (From Topology)	T: a+b domain in acetyl-CoA synthetase-like proteins	F: AMP-binding_C	ECOD (1.6)
A	Condensation_N	e4zxiA7	A: a+b complex topology	X: CoA-dependent acyltransferases (From Topology)	H: CoA-dependent acyltransferases (From Topology)	T: CoA-dependent acyltransferases	F: Condensation_N	ECOD (1.6)
A	Condensation_C_2	e4zxiA6	A: a+b complex topology	X: CoA-dependent acyltransferases (From Topology)	H: CoA-dependent acyltransferases (From Topology)	T: CoA-dependent acyltransferases	F: Condensation_C_2	ECOD (1.6)
A	Hydrolase_4_1	e4zxiA8	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	AMP-binding_1st	e4zxiA4	A: a/b three-layered sandwiches	X: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	H: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	T: Rossmann-like domain in Acetyl-CoA synthetase-like proteins	F: AMP-binding_1st	ECOD (1.6)
A	AMP-binding_2nd	e4zxiA3	A: a/b three-layered sandwiches	X: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	H: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	T: Rossmann-like domain in Acetyl-CoA synthetase-like proteins	F: AMP-binding_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00501	AMP-binding enzyme (AMP-binding)	AMP-binding enzyme	-	Family
A	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
A	PF00668	Condensation domain (Condensation)	Condensation domain	-	Family
A	PF13193	AMP-binding enzyme C-terminal domain (AMP-binding_C)	AMP-binding enzyme C-terminal domain	This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.	Domain
A	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Tyrocidine synthetase 3	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding vitamin binding amide binding modified amino acid binding phosphopantetheine binding catalytic activity	secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.