6XND | pdb_00006xnd

Avidin-Biotin-Phenol

• PDB DOI: https://doi.org/10.2210/pdb6XND/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Gallus gallus
• Expression System: Gallus gallus
• Mutation(s): Yes 


• Deposited: 2020-07-02 Released: 2021-03-03 
• Deposition Author(s): Ahmadvand, P., Kang, C.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

A Ligand-Directed Nitrophenol Carbonate for Transient in situ Bioconjugation and Drug Delivery

Burt, A.J., Ahmadvand, P., Opp, L.K., Ryan, A.T., Kang, C., Mancini, R.J.

(2020) ChemMedChem 15: 2004-2009

• DOI: https://doi.org/10.1002/cmdc.202000655

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.03 kDa 
• Atom Count: 4,182 
• Modeled Residue Count: 484 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B, C, D	128	Gallus gallus	Mutation(s): 1  Gene Names: AVD
UniProt
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V8M (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide C18 H24 N4 O5 S GGNOUTGIVZKNRF-KMFMINBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.526	α = 90
b = 79.254	β = 105.46
c = 74.683	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Ahmadvand, P., Kang, C.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1804699

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.0: 2024-11-06
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary