9WF1 | pdb_00009wf1

PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus

• PDB DOI: https://doi.org/10.2210/pdb9WF1/pdb

• Classification: TRANSFERASE
• Organism(s): Ancylobacter lacus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-20 Released: 2026-02-04 
• Deposition Author(s): Lin, S., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

Engineered omega-Transaminase Enables Remote Stereocontrol in the Synthesis of Chiral Pharmaceutical N-Heterocyclic Amines with Nonadjacent Stereocenters

Zhang, Y., Wang, X., Yin, X., Huang, T., Lin, S.

(2026) ACS Catal 16: 587-598

• DOI: https://doi.org/10.1021/acscatal.5c07044

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 144.47 kDa 
• Atom Count: 11,244 
• Modeled Residue Count: 1,271 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omega-Transaminase	A, B [auth D], C [auth F], D [auth H]	320	Ancylobacter lacus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EVZ (Subject of Investigation/LOI)	E [auth A], F [auth D], G [auth F], H	~{tert}-butyl (2~{S})-2-methyl-5-oxidanylidene-piperidine-1-carboxylate C11 H19 N O3 CSTUUOYWLVVNLE-QMMMGPOBSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B [auth D], C [auth F], D [auth H]	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.83	α = 74.64
b = 72.45	β = 85.69
c = 84.32	γ = 69.92

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Lin, S., Zhang, Y.

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

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release