3VHM

Crystal structure of NPC-biotin-avidin complex

• PDB DOI: https://doi.org/10.2210/pdb3VHM/pdb

• Classification: BIOTIN-BINDING PROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2011-08-29 Released: 2011-12-28 
• Deposition Author(s): Terai, T., Maki, E., Sugiyama, S., Takahashi, Y., Matsumura, H., Mori, Y., Nagano, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.25 kDa 
• Atom Count: 4,241 
• Modelled Residue Count: 488 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B, C, D	123	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPK	E [auth A], I [auth B], M [auth C], P [auth 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
NAG	F [auth A], J [auth B], N [auth C], Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], R [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
NPK	Binding MOAD:  3VHM	Ka: 1.50e+4 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.02	α = 90
b = 73.535	β = 120.02
c = 81.18	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary