5ZIO | pdb_00005zio

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.137 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8Z	D [auth A]	L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.137 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Zhang, H., Hao, Q.

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

Revision History  

• 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