8HYC | pdb_00008hyc

Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-(2-(thiophen-2-yl)ethyl)thiazole-4-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb8HYC/pdb

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


• Deposited: 2023-01-06 Released: 2024-06-19 
• Deposition Author(s): Yan, Y.-H., Zhu, K.-R., Li, G.-B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

2-Aminothiazole-4-carboxylic acids as cross-class metallo-beta-lactamase inhibitors by mimicking beta-lactam hydrolysate binding

Yan, Y.-H., Zhu, K.-R., Yang, L.-L., Li, G.-B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.92 kDa 
• Atom Count: 3,916 
• Modeled Residue Count: 482 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A, B	241	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
60J (Subject of Investigation/LOI)	E [auth A], H [auth B]	2-azanyl-5-(2-thiophen-2-ylethyl)-1,3-thiazole-4-carboxylic acid C10 H10 N2 O2 S2 SUXXXFYCNZRVEM-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.053	α = 90
b = 78.384	β = 90
c = 131.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PHASER	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Yan, Y.-H., Zhu, K.-R., Li, G.-B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291
National Natural Science Foundation of China (NSFC)	China	82122065
National Natural Science Foundation of China (NSFC)	China	82073698

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release