7S6C | pdb_00007s6c

CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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)
G	C1-set_4	e7s6cG2	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)
G	V-set	e7s6cG1	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)
F	C1-set_4	e7s6cF2	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)
F	V-set	e7s6cF1	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)
H	C1-set_1	e7s6cH2	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)
H	V-set_12	e7s6cH1	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)
E	C1-set_1	e7s6cE2	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)
E	V-set_12	e7s6cE1	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)
D	PP-binding	e7s6cD1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
C	KR_1_SDR_x	e7s6cC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: KR_1_SDR_x	ECOD (1.6)
C	adh_short_C2_1	e7s6cC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: adh_short_C2_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	3.40.47.10	Alpha Beta	3-Layer(aba) Sandwich	Peroxisomal Thiolase	Chain A, domain 1	CATH (utative)
B	3.30.70.3290	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
B	3.40.366.10	Alpha Beta	3-Layer(aba) Sandwich	Malonyl-Coenzyme A Acyl Carrier Protein	domain 2	CATH (utative)
A	3.40.47.10	Alpha Beta	3-Layer(aba) Sandwich	Peroxisomal Thiolase	Chain A, domain 1	CATH (utative)
A	3.30.70.3290	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
A	3.40.366.10	Alpha Beta	3-Layer(aba) Sandwich	Malonyl-Coenzyme A Acyl Carrier Protein	domain 2	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F, G	Light Chain	IGKV2	Kappa	6-deoxyerythronolide-b synthase erya2, modules 3 and 4,lsd14 polyketide synthase fusion	SAbDab (2025-10-31)
E, H	Heavy Chain	IGHV3	-	6-deoxyerythronolide-b synthase erya2, modules 3 and 4,lsd14 polyketide synthase fusion	SAbDab (2025-10-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	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, B, C, D	PF16197	Ketoacyl-synthetase C-terminal extension (KAsynt_C_assoc)	Ketoacyl-synthetase C-terminal extension	-	Family
A, B, C, D	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, B, C, D	PF08659	KR domain (KR)	KR domain	-	Family
A, B, C, D	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
F, G	Fab 1B2 light chain	-	-	-
E, H	Fab 1B2 heavy chain	-	-	-
A, B, C, D	6-deoxyerythronolide-B synthase EryA2, modules 3 and 4, Lsd14 Polyketide synthase fusion	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 catalytic activity fatty acid synthase activity oxidoreductase activity erythronolide synthase activity	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid 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 biosynthetic process small molecule metabolic process metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid 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 biosynthetic 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 antibiotic metabolic process polyketide biosynthetic process secondary metabolite biosynthetic process lactone metabolic process lactone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
A, B, C, D	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
A, B, C, D	IPR015083	Polyketide synthase NorB/C/GfsB-E-like, docking domain	Domain
A, B, C, D	IPR006162	Phosphopantetheine attachment site	PTM
A, B, C, D	IPR057326	Ketoreductase domain	Domain
A, B, C, D	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
A, B, C, D	IPR050091	Polyketide and Nonribosomal Peptide Biosynthesis Enzymes	Family
A, B, C, D	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
A, B, C, D	IPR036736	ACP-like superfamily	Homologous Superfamily
A, B, C, D	IPR014043	Acyl transferase domain	Domain
A, B, C, D	IPR041618	Polyketide synthase dimerisation element domain	Domain
A, B, C, D	IPR032821	Polyketide synthase, C-terminal extension	Domain
A, B, C, D	IPR009081	Phosphopantetheine binding ACP domain	Domain
A, B, C, D	IPR020806	Polyketide synthase-like, phosphopantetheine-binding domain	Domain
A, B, C, D	IPR036299	Polyketide synthase, docking domain superfmaily	Homologous Superfamily
A, B, C, D	IPR013968	Polyketide synthase-like, ketoreductase domain	Domain
A, B, C, D	IPR016039	Thiolase-like	Homologous Superfamily
A, B, C, D	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR018201	Beta-ketoacyl synthase, active site	Active Site
A, B, C, D	IPR014030	Beta-ketoacyl synthase-like, N-terminal	Domain
A, B, C, D	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
A, B, C, D	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
A, B, C, D	IPR015083	Polyketide synthase NorB/C/GfsB-E-like, docking domain	Domain
A, B, C, D	IPR006162	Phosphopantetheine attachment site	PTM
A, B, C, D	IPR013154	Alcohol dehydrogenase-like, N-terminal	Domain
A, B, C, D	IPR036347	Erythronolide synthase, docking domain superfamily	Homologous Superfamily
A, B, C, D	IPR049552	Polyketide synthase, dehydratase domain, N-terminal	Domain
A, B, C, D	IPR049900	Polyketide synthase, dehydratase domain	Domain
A, B, C, D	IPR049551	Polyketide synthase, dehydratase domain, C-terminal	Domain
A, B, C, D	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
A, B, C, D	IPR050091	Polyketide and Nonribosomal Peptide Biosynthesis Enzymes	Family
A, B, C, D	IPR015357	Erythronolide synthase EryA2, docking domain	Domain
A, B, C, D	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
A, B, C, D	IPR020807	Polyketide/metazoan fatty acid synthase-like, dehydratase domain	Domain
A, B, C, D	IPR036736	ACP-like superfamily	Homologous Superfamily
A, B, C, D	IPR014043	Acyl transferase domain	Domain
A, B, C, D	IPR020843	Enoylreductase domain	Domain
A, B, C, D	IPR032821	Polyketide synthase, C-terminal extension	Domain
A, B, C, D	IPR011032	GroES-like superfamily	Homologous Superfamily
A, B, C, D	IPR009081	Phosphopantetheine binding ACP domain	Domain
A, B, C, D	IPR020806	Polyketide synthase-like, phosphopantetheine-binding domain	Domain
A, B, C, D	IPR013968	Polyketide synthase-like, ketoreductase domain	Domain
A, B, C, D	IPR016039	Thiolase-like	Homologous Superfamily
A, B, C, D	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR018201	Beta-ketoacyl synthase, active site	Active Site
A, B, C, D	IPR014030	Beta-ketoacyl synthase-like, N-terminal	Domain
A, B, C, D	IPR042104	Polyketide synthase, dehydratase domain superfamily	Homologous Superfamily
A, B, C, D	IPR055123	Polyketide synthase extender module SpnB-like, Rossmann fold domain	Domain

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CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

7S6C | pdb_00007s6c