5N0H

Crystal structure of NDM-1 in complex with hydrolyzed meropenem - new refinement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 5N0H

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 53138.18

Macromolecule Entities
Molecule Chains Length Organism Details
Metallo-beta-lactamase type 2 A, B 245 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Gene Name(s): blaNDM-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8YL
Query on 8YL

A (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene- butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin- 3-yl]sulfanyl-3-methyl-2,3-dihydro-1H-pyrrole- 5-carboxylic acid
Meropenem, hydrolyzed form (Synonym)
C17 H27 N3 O6 S
ILVWWUFTACAPIZ-PQTSNVLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
A, B L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.155
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 106.00 α = 90.00
b = 106.00 β = 90.00
c = 92.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-03
  • Released Date: 2017-04-05
  • Deposition author(s): Raczynska, J.E., Shabalin, I.G., Jaskolski, M., Minor, W., Wlodawer, A., King, D.T., Strynadka, N.C.J.

Revision History

  • Version 1_0: 2017-04-05

    Type: Initial release

  • Version 2_0: 2017-12-13

    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary