6C9U

Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth L]	d6c9ul1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	KASAT domain-like	8055827	3002319	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FabD/lysophospholipase-like	8055831	3001121	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	KASAT domain-like	8055827	3002319	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiolase-like	8055829	3000122	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FabD/lysophospholipase-like	8055831	3001121	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Probable ACP-binding domain of malonyl-CoA ACP transacylase	8055834	3001224	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Acyl_transf_1_2nd_1	e6c9uA2	A: a+b two layers	X: Alpha-beta plaits	H: Probable ACP-binding domain of malonyl-CoA ACP transacylase (From Topology)	T: Probable ACP-binding domain of malonyl-CoA ACP transacylase	F: Acyl_transf_1_2nd_1	ECOD (1.6)
A	PksD_2	e6c9uA3	A: a+b two layers	X: KS-MAT linker domain in fatty acid synthase (From Topology)	H: KS-MAT linker domain in fatty acid synthase (From Topology)	T: KS-MAT linker domain in fatty acid synthase	F: PksD_2	ECOD (1.6)
A	Acyl_transf_1_1st	e6c9uA6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: Acyl_transf_1_1st	ECOD (1.6)
A	ketoacyl-synt	e6c9uA4	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: ketoacyl-synt	ECOD (1.6)
A	Ketoacyl-synt_C	e6c9uA5	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: Ketoacyl-synt_C	ECOD (1.6)
B [auth L]	C1-set_4	e6c9uL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e6c9uL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth H]	C1-set_1	e6c9uH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth H]	V-set_12	e6c9uH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth L]	Fab 1B2	L-KAPPA	Homo sapiens (human)	IGKV2-2801, IGKV2D-2801, IGKJ301, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C [auth H]	Fab 1B2	VH-CH1	Homo sapiens (human)	IGHV3-4904, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV2	Kappa	6-deoxyerythronolide-b synthase erya2, modules 3 and 4	SAbDab (2024-04-19)
C [auth H]	Heavy Chain	IGHV3	-	6-deoxyerythronolide-b synthase erya2, modules 3 and 4	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02801	Beta-ketoacyl synthase, C-terminal domain (Ketoacyl-synt_C)	Beta-ketoacyl synthase, C-terminal domain	The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.	Domain
A	PF00109	Beta-ketoacyl synthase, N-terminal domain (ketoacyl-synt)	Beta-ketoacyl synthase, N-terminal domain	The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains m ...	The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine [1].	Domain
A	PF16197	Ketoacyl-synthetase C-terminal extension (KAsynt_C_assoc)	Ketoacyl-synthetase C-terminal extension	-	Family
A	PF08990	Erythronolide synthase docking domain (Docking)	Erythronolide synthase docking domain	Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants [1]. Type I modular PKSs are the large, multifunctional enzymes responsible for the pro ...	Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants [1]. Type I modular PKSs are the large, multifunctional enzymes responsible for the production of a diverse family of structurally rich and often biologically active natural products. The efficiency of acyl transfer at the interfaces of the individual PKS proteins is thought to be governed by helical regions, termed docking domains (dd). Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function [1].	Domain
A	PF00698	Acyl transferase domain (Acyl_transf_1)	Acyl transferase domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	6-deoxyerythronolide-B synthase EryA2, modules 3 and 4	oxidoreductase activity catalytic activity vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding acyltransferase activity 3-oxoacyl-[acyl-carrier-protein] synthase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity erythronolide synthase activity	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular lipid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process macrolide biosynthetic process polyketide metabolic process macrolide metabolic process secondary metabolic process antibiotic biosynthetic process organic cyclic compound metabolic process antibiotic metabolic process polyketide biosynthetic process secondary metabolite biosynthetic process lactone metabolic process lactone biosynthetic process organic cyclic compound biosynthetic process	-
B [auth L]	Light chain of Fab 1B2	-	-	-
C [auth H]	Heavy chain of Fab 1B2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
A	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
A	IPR006162	Phosphopantetheine attachment site	PTM
A	IPR013154	Alcohol dehydrogenase-like, N-terminal	Domain
A	IPR020807	Polyketide synthase, dehydratase domain	Domain
A	IPR014030	Beta-ketoacyl synthase, N-terminal	Domain
A	IPR036347	Erythronolide synthase, docking domain superfamily	Homologous Superfamily
A	IPR049552	Polyketide synthase, dehydratase domain, N-terminal	Domain
A	IPR049551	Polyketide synthase, dehydratase domain, C-terminal	Domain
A	IPR020843	Polyketide synthase, enoylreductase domain	Domain
A	IPR013968	Polyketide synthase, ketoreductase domain	Domain
A	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
A	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
A	IPR014043	Acyl transferase	Domain
A	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
A	IPR036736	ACP-like superfamily	Homologous Superfamily
A	IPR015083	Polyketide synthase, docking domain	Domain
A	IPR032821	Polyketide synthase, C-terminal extension	Domain
A	IPR011032	GroES-like superfamily	Homologous Superfamily
A	IPR009081	Phosphopantetheine binding ACP domain	Domain
A	IPR016039	Thiolase-like	Homologous Superfamily
A	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR018201	Beta-ketoacyl synthase, active site	Active Site
A	IPR042104	Polyketide synthase, dehydratase domain superfamily	Homologous Superfamily
A	IPR015357	Erythronolide synthase, docking	Domain