2BZD

Galactose recognition by the carbohydrate-binding module of a bacterial sialidase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 2BZD

Classification: HYDROLASE

Total Structure Weight: 193607.52

Macromolecule Entities
Molecule Chains Length Organism Details
BACTERIAL SIALIDASE A, B, C 601 Micromonospora viridifaciens EC#: 3.2.1.18 IUBMB
Fragment: RESIDUES 47-647
Mutation: E260A
Gene Name(s): nedA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A, B, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GAL N/A in BindingDB
Kd: 1000000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.193
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 141.46 α = 90.00
b = 141.46 β = 90.00
c = 158.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-16
  • Released Date: 2005-08-19
  • Deposition author(s): Newstead, S.L., Taylor, G.
  • Previous versions: 2BQ9

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance