2W68

ENHANCING THE RECEPTOR AFFINITY OF THE SIALIC ACID-BINDING DOMAIN OF VIBRIO CHOLERAE SIALIDASE THROUGH MULTIVALENCY

Structural Biology Knowledgebase: 2W68 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2W68

Classification: HYDROLASE

Total Structure Weight: 65247.95

Macromolecule Entities
Molecule Chains Length Organism Details
SIALIDASE A, B, C 195 Vibrio cholerae EC#: 3.2.1.18 IUBMB
Fragment: CBM40 DOMAIN, RESIDUES 25-216
Gene Name(s): nanH VC_1784
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A, B, C BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A, B, C BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SIA N/A in BindingDB
N/A in BindingMoad
Kd: 18000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.215
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 138.60 α = 90.00
b = 197.62 β = 90.00
c = 82.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-12-17
  • Released Date: 2008-12-30
  • Deposition author(s): Connaris, H., Crocker, P.R., Taylor, G.L.

Revision History

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