3VGW

Crystal structure of monoAc-biotin-avidin complex

Structural Biology Knowledgebase: 3VGW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 3VGW

Classification: BIOTIN-BINDING PROTEIN

Total Structure Weight: 114945.48

Macromolecule Entities
Molecule Chains Length Organism Details
Avidin A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 123 Gallus gallus Fragment: UNP residues 25-147
Gene Name(s): AVD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H- thieno[3,4-d]imidazol-4-yl]pentanoic acid
C12 H18 N2 O4 S
LXKFOEIWWHPOIN-QXEWZRGKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D, E, F, G, H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F, G, H SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NVZ N/A in BindingDB
Ka: 200000 M-1  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.190
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 116.01 α = 90.00
b = 81.22 β = 92.47
c = 74.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-21
  • Released Date: 2011-12-28
  • Deposition author(s): Terai, T., Maki, E., Sugiyama, S., Takahashi, Y., Matsumura, H., Mori, Y., Nagano, T.

Revision History

No revisions since initial release