3VHI

Crystal structure of monoZ-biotin-avidin complex

Structural Biology Knowledgebase: 3VHI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VHI

Classification: BIOTIN-BINDING PROTEIN

Total Structure Weight: 57556.96

Macromolecule Entities
Molecule Chains Length Organism Details
Avidin A, B, C, D 122 Gallus gallus Fragment: UNP residues 26-147
Gene Name(s): AVD

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

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
VHI
Query on VHI

A, B, C, D 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2- oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid
C18 H22 N2 O5 S
BWNGWJMPVBQLHD-DZKIICNBSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VHI N/A in BindingDB
Ka: 2.3e+06 M-1  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.184
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 130.78 α = 90.00
b = 73.46 β = 120.05
c = 81.25 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