1Y52

structure of insect cell (Baculovirus) expressed AVR4 (C122S)-biotin complex

• PDB DOI: https://doi.org/10.2210/pdb1Y52/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Gallus gallus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2004-12-02 Released: 2005-05-24 
• Deposition Author(s): Eisenberg-Domovich, Y., Hytonen, V.P., Wilchek, M., Bayer, E.A., Kulomaa, M.S., Livnah, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 29.69 kDa 
• Atom Count: 2,104 
• Modelled Residue Count: 240 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin-related protein 4/5	A [auth X], B [auth Y]	126	Gallus gallus	Mutation(s): 1  Gene Names: AVR4
UniProt
Find proteins for P56734 (Gallus gallus) Explore P56734  Go to UniProtKB:  P56734

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	E [auth X], H [auth Y]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
NAG	C [auth X], D [auth X], F [auth Y], G [auth Y]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	Binding MOAD:  1Y52	Kd: 64 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.963	α = 90
b = 80.963	β = 90
c = 140.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Eisenberg-Domovich, Y., Hytonen, V.P., Wilchek, M., Bayer, E.A., Kulomaa, M.S., Livnah, O.

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.5: 2024-01-03
  Changes: Data collection