9KK9 | pdb_00009kk9

Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP

PDB DOI: https://doi.org/10.2210/pdb9KK9/pdb

Classification: TRANSFERASE
Organism(s): Vibrio vulnificus NBRC 15645 = ATCC 27562
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-13 Released: 2025-11-19
Deposition Author(s): Ma, Q., Han, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.189 (Depositor), 0.199 (DCC)
R-Value Work:
0.167 (Depositor), 0.169 (DCC)
R-Value Observed:
0.168 (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

Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP

Ma, Q., Han, M.

To be published.

Macromolecule Content

Total Structure Weight: 122.51 kDa
Atom Count: 8,772
Modeled Residue Count: 1,086
Deposited Residue Count: 1,107
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminoethylphosphonate--pyruvate transaminase	A, B, C	369	Vibrio vulnificus NBRC 15645 = ATCC 27562	Mutation(s): 0 Gene Names: phnW, VVA0476 EC: 2.6.1.37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P7I (Subject of Investigation/LOI) Query on P7I Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(2-aminoethyl)phosphonic acid C₂ H₈ N O₃ P QQVDJLLNRSOCEL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.189 (Depositor), 0.199 (DCC)
R-Value Work: 0.167 (Depositor), 0.169 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.248	α = 90
b = 94.945	β = 90.51
c = 91.184	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

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: 2025-11-19
Type: Initial release

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.