2VK7

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Structural Biology Knowledgebase: 2VK7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.131

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VK7

Classification: HYDROLASE

Total Structure Weight: 101595.63

Macromolecule Entities
Molecule Chains Length Organism Details
EXO-ALPHA-SIALIDASE A, B 452 Clostridium perfringens EC#: 3.2.1.18 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 243-694
Gene Name(s): nanH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro- alpha-L-manno-non-2-ulopyranosonic acid
3-FLUOROSIALIC ACID (Synonym)
C11 H18 F N O9
ALJLGESFXXDPKH-RISWTRDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.131
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.60 α = 90.00
b = 97.40 β = 91.00
c = 72.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-17
  • Released Date: 2008-01-22
  • Deposition author(s): Newstead, S.L., Potter, J.A., Wilson, J.C., Xu, G., Chien, C.H., Watts, A.G., Withers, S.G., Taylor, G.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4