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)

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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

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

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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	3D Interactions
A1EVZ (Subject of Investigation/LOI) Query on A1EVZ Download:Ideal Coordinates CCD File SDF format, chain H SDF format, chain G [auth F] SDF format, chain F [auth D] SDF format, chain E [auth A] MOL2 format, chain H MOL2 format, chain G [auth F] MOL2 format, chain F [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H mmCIF format, chain G [auth F] mmCIF format, chain F [auth D] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth D] Focus chain G [auth F] Focus chain H Interactions & Density Focus chain E [auth A] Focus chain F [auth D] Focus chain G [auth F] Focus chain H

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on 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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.