Macromolecule Content

Total Structure Weight: 26.65 kDa
Atom Count: 2,165
Modelled Residue Count: 231
Deposited Residue Count: 246
Unique protein chains: 1

7UYC

Inhibitor bound VIM1

PDB DOI: https://doi.org/10.2210/pdb7UYC/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-06 Released: 2023-05-24
Deposition Author(s): Fischmann, T.O., Scapin, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.164
R-Value Work: 0.152
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

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

Literature

Inhibitor bound VIM1

Fischmann, T.O., Scapin, G.

To be published.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-1	A	246	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245
UniProt
Find proteins for Q9XAY4 (Pseudomonas aeruginosa) Explore Q9XAY4 Go to UniProtKB: Q9XAY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9XAY4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OJR (Subject of Investigation/LOI) Query on OJR Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(2P)-4'-(piperidin-4-yl)-4-[(piperidin-4-yl)methyl]-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide C₂₄ H₃₁ N₇ O₂ S LHOHTNKBXFSQBC-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.164
R-Value Work: 0.152
R-Value Observed: 0.152
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.507	α = 90
b = 67.927	β = 91.67
c = 40.165	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
BUSTER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Fischmann, T.O.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.