9SUC | pdb_00009suc

High Throughput Crystallography to Combat Antibiotic Resistance - VIM2 with compound x0797

PDB DOI: https://doi.org/10.2210/pdb9SUC/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-27 Released: 2026-10-07
Deposition Author(s): Wang, D.Y., Brem, J., Collins, P.M., vonDelft, F., Allen, M.D., Schofield, C.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free:
0.157 (Depositor), 0.165 (DCC)
R-Value Work:
0.125 (Depositor), 0.142 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

High Throughput Crystallography to Combat Antibiotic Resistance - VIM2 with compound x0797

Wang, D.Y., Brem, J., Collins, P.M., vonDelft, F., Allen, M.D., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 52.56 kDa
Atom Count: 4,372
Modeled Residue Count: 464
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	242	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaVIM-2, bla vim-2, blm, PAERUG_P19_London_7_VIM_2_05_10_01672 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0 Go to UniProtKB: Q9K2N0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JQA( Subject of Investigation/LOI) Query on A1JQA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth A], L [auth B], M [auth B]	6-pyrrol-1-ylpyridine-2-carboxylic acid C₁₀ H₈ N₂ O₂ WSBDMSCYANSHMQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	G [auth A], H [auth A], N [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.157 (Depositor), 0.165 (DCC)
R-Value Work: 0.125 (Depositor), 0.142 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.56	α = 90
b = 79.81	β = 130.25
c = 68.57	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Schofield, C.J.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	099141/Z/12/Z

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release