4H0D

New Delhi Metallo-beta-Lactamase-1 Complexed with Mn from Klebsiella pneumoniae

Structural Biology Knowledgebase: 4H0D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.158
  • R-Value Work: 0.120

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H0D

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 52764.93

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase NDM-1 A, B 243 Klebsiella pneumoniae EC#: 3.5.2.6 IUBMB
Gene Name(s): blaNDM-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZZ7
Query on ZZ7

A, B (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]- 5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form) (Synonym)
C16 H21 N3 O5 S
KDAWOPKDXRJNHV-MPPDQPJWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 39.10 α = 90.00
b = 78.61 β = 90.00
c = 133.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-07
  • Released Date: 2012-09-26
  • Deposition author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Babnigg, J., Binkowski, T.A., Mire, J., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MT

Revision History

No revisions since initial release