2VW1

CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE

Structural Biology Knowledgebase: 2VW1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VW1

Classification: HYDROLASE

Total Structure Weight: 78164.91

Macromolecule Entities
Molecule Chains Length Organism Details
SIALIDASE B A 697 Streptococcus pneumoniae EC#: 3.2.1.18 IUBMB
Gene Name(s): nanB SP_1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAN N/A in BindingDB
Ki: 300000 nM  BindingMOAD
Ki: 300000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.192
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 76.60 α = 90.00
b = 82.70 β = 90.00
c = 117.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-13
  • Released Date: 2008-06-24
  • Deposition author(s): Xu, G., Potter, J.A., Russell, R.J.M., Oggioni, M.R., Andrew, P.W., Taylor, G.L.

Revision History

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