9KA6 | pdb_00009ka6

Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with acyl-ACP from E. coli

• PDB DOI: https://doi.org/10.2210/pdb9KA6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-28 Released: 2025-09-10 
• Deposition Author(s): Zhang, L., Zhang, L., Cai, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

The Molecular Basis of the beta-Ketoacyl-ACP Synthase FabH in Catalyzing C-C Bond Formation of Acetoacetyl-ACP

Cai, C., Huang, Y., Zhang, L., Zhang, L.

(2025) ACS Catal 15: 5028-5038

• DOI: https://doi.org/10.1021/acscatal.5c01167

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 81.36 kDa 
• Atom Count: 6,386 
• Modeled Residue Count: 711 
• Deposited Residue Count: 758 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-ketoacyl-[acyl-carrier-protein] synthase III	A, B	337	Escherichia coli	Mutation(s): 1  Gene Names: fabH, b1091, JW1077 EC: 2.3.1.180
UniProt
Find proteins for P0A6R0 (Escherichia coli (strain K12)) Explore P0A6R0  Go to UniProtKB:  P0A6R0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C	84	Escherichia coli	Mutation(s): 0  Gene Names: acpP, b1094, JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6VG (Subject of Investigation/LOI)	D [auth C]	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate C13 H25 N2 O8 P S AJFWMDFTVVFMHY-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.464	α = 90
b = 143.325	β = 90
c = 140.727	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Zhang, L., Zhang, L., Cai, C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22477077

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release