5J72

Cwp6 from Clostridium difficile

Structural Biology Knowledgebase: 5J72 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 5J72

Classification: HYDROLASE

Total Structure Weight: 139601.17

Macromolecule Entities
Molecule Chains Length Organism Details
Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6 A, B 638 Clostridioides difficile EC#: 3.5.1.28 IUBMB
Gene Name(s): cwp6 CD630_27840
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CIT
Query on CIT

B CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-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)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.178
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.36 α = 90.00
b = 212.92 β = 90.00
c = 84.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-04-05
  • Released Date: 2017-02-08
  • Deposition author(s): Renko, M., Usenik, A., Turk, D.

Revision History

  • 2017-03-22
    Type: Data collection | Details: Data collection
  • 2017-03-22
    Type: Citation | Details: Citation
  • 2017-03-08
    Type: Refinement description | Details: added version for refmac