4U4L

Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb4U4L/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-23 Released: 2014-08-20
Deposition Author(s): Kosmopoulou, M., Hinchliffe, P., Spencer, J.
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.182
R-Value Work: 0.154
R-Value Observed: 0.155

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor

Kosmopoulou, M., Hinchliffe, P., Spencer, J.

To be published.

Macromolecule Content

Total Structure Weight: 105.71 kDa
Atom Count: 7,459
Modelled Residue Count: 907
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase NDM-1	A, B, C, D	246	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422 Go to UniProtKB: C7C422
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7C422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3C7 Query on 3C7 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	G [auth A], J [auth B], N [auth C], R [auth D]	(3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid C₇ H₁₁ N O₂ S₃ ZTWVMVSSSBGFHH-JKUQZMGJSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	M [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain M [auth C] Focus chain Q [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.182
R-Value Work: 0.154
R-Value Observed: 0.155
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.57	α = 87.39
b = 69.023	β = 88.21
c = 69.646	γ = 76.75

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-08-20

Deposition Author(s):

Kosmopoulou, M.

Hinchliffe, P.

Spencer, J.

Funding Organization	Location	Grant Number
National Institutes of Health	United States	AI100560

Revision History (Full details and data files)

Version 1.0: 2014-08-20
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description