2VK6

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Structural Biology Knowledgebase: 2VK6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.160

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VK6

Classification: HYDROLASE

Total Structure Weight: 51029.18

Macromolecule Entities
Molecule Chains Length Organism Details
EXO-ALPHA-SIALIDASE A 452 Clostridium perfringens EC#: 3.2.1.18 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 243-694
Mutation: G1393S
Gene Name(s): nanH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAN N/A in BindingDB
N/A in BindingMoad
Ki: 5000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.160
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.37 α = 90.00
b = 71.05 β = 90.00
c = 98.90 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