1M2X

Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum in complex with the inhibitor D-captopril

Structural Biology Knowledgebase: 1M2X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1M2X

Classification: HYDROLASE

Total Structure Weight: 103535.95

Macromolecule Entities
Molecule Chains Length Organism Details
class B carbapenemase BlaB-1 A, B, C, D 223 Elizabethkingia meningoseptica EC#: 3.5.2.6 IUBMB
Gene Name(s): blaB1 blaB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE- 2-CARBOXYLIC ACID
C9 H15 N O3 S
FAKRSMQSSFJEIM-RNFRBKRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MCO N/A in BindingDB
Ki: 85000 nM  BindingMOAD
Ki: 70000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.190
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 159.68 α = 90.00
b = 159.68 β = 90.00
c = 97.82 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-26
  • Released Date: 2003-07-29
  • Deposition author(s): Garcia-Saez, I., Dideberg, O.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update