3SPU | pdb_00003spu

apo NDM-1 Crystal Structure

PDB DOI: https://doi.org/10.2210/pdb3SPU/pdb

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

Deposited: 2011-07-03 Released: 2011-08-03
Deposition Author(s): Strynadka, N.C.J., King, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.253 (Depositor)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of New Delhi metallo-beta-lactamase reveals molecular basis for antibiotic resistance

King, D., Strynadka, N.

(2011) Protein Sci 20: 1484-1491

PubMed: 21774017 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.697
Primary Citation Related Structures:
3SPU

PubMed Abstract:
β-Lactams are the most commonly prescribed class of antibiotics and have had an enormous impact on human health. Thus, it is disquieting that an enzyme called New Delhi metallo-β-lactamase-1 (NDM-1) can confer Enterobacteriaceae with nearly complete resistance to all β-lactam antibiotics including the carbapenams. We have determined the crystal structure of Klebsiella pneumoniae apo-NDM-1 to 2.1-Å resolution. From the structure, we see that NDM-1 has an expansive active site with a unique electrostatic profile, which we propose leads to a broader substrate specificity. In addition, NDM-1 undergoes important conformational changes upon substrate binding. These changes have not been previously observed in metallo-β-lactamase enzymes and may have a direct influence on substrate recognition and catalysis.

Organizational Affiliation

Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.

Macromolecule Content

Total Structure Weight: 141.81 kDa
Atom Count: 9,130
Modeled Residue Count: 1,160
Deposited Residue Count: 1,325
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase NDM-1	A, B, C, D, E	265	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7C422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [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 D] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [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 D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [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 D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C]	F [auth A] G [auth A] H [auth B] I [auth B] J [auth C] F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253 (Depositor)
R-Value Work: 0.216 (Depositor)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.536	α = 70.32
b = 73.904	β = 75.86
c = 77.407	γ = 65.3

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Strynadka, N.C.J.

King, D.T.

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2011-09-14
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 2.0: 2019-10-30
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description