3VHH

Crystal structure of DiMe-biotin-avidin complex

Structural Biology Knowledgebase: 3VHH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 3VHH

Classification: BIOTIN-BINDING PROTEIN

Total Structure Weight: 57416.81

Macromolecule Entities
Molecule Chains Length Organism Details
Avidin A, B, C, D 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
VHH
Query on VHH

A, B, C, D 5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro- 1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
C12 H20 N2 O3 S
PECDAVNFXWSGFV-QXEWZRGKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D 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 SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VHH N/A in BindingDB
Ka: 4e+08 M-1  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.200
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 129.97 α = 90.00
b = 73.51 β = 119.64
c = 81.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-25
  • 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