3VHM

Crystal structure of NPC-biotin-avidin complex

Structural Biology Knowledgebase: 3VHM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 3VHM

Classification: BIOTIN-BINDING PROTEIN

Total Structure Weight: 58253.27

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
NPK
Query on NPK

A, B, C, D 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol- 5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4- d]imidazol-4-yl]pentanoic acid
C20 H23 N3 O9 S
MVOCLTWEOIJKEV-JTWAPGJUSA-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 %)
NPK N/A in BindingDB
Ka: 15000 M-1  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.02 α = 90.00
b = 73.54 β = 120.02
c = 81.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-29
  • 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