4HL2

New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin

PDB DOI: https://doi.org/10.2210/pdb4HL2/pdb

Classification: Hydrolase/Antibiotic
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-10-15 Released: 2012-12-12
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Mire, J., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.134

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin

Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Mire, J., Sacchettini, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 52.93 kDa
Atom Count: 4,674
Modelled Residue Count: 485
Deposited Residue Count: 486
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	243	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
ZZ7 Query on ZZ7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C₁₆ H₂₁ N₃ O₅ S KDAWOPKDXRJNHV-MPPDQPJWSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A], E [auth A], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth B] F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M34HL2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.19	α = 90
b = 79.171	β = 90
c = 134.473	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
SHELX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Refinement description
Version 1.2: 2019-08-14
Changes: Data collection
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description