5ZIO

Crystal structure of NDM-1 in complex with L-captopril

PDB DOI: https://doi.org/10.2210/pdb5ZIO/pdb

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

Deposited: 2018-03-16 Released: 2019-03-20
Deposition Author(s): Zhang, H., Hao, Q.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.137
R-Value Work: 0.123
R-Value Observed: 0.124

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors

Ma, G., Wang, S., Wu, K., Zhang, W., Ahmad, A., Hao, Q., Lei, X., Zhang, H.

(2020) Bioorg Med Chem 29

DOI: https://doi.org/10.1016/j.bmc.2020.115902

Macromolecule Content

Total Structure Weight: 25.98 kDa
Atom Count: 2,059
Modelled Residue Count: 228
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	242	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X8Z Query on X8Z Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	L-CAPTOPRIL C₉ H₁₅ N O₃ S FAKRSMQSSFJEIM-RQJHMYQMSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.137
R-Value Work: 0.123
R-Value Observed: 0.124
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.506	α = 90
b = 59.948	β = 98.06
c = 41.904	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Zhang, H.

Hao, Q.

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31670753

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2020-12-16
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5ZIO

Crystal structure of NDM-1 in complex with L-captopril

Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)