1WBI

AVR2

PDB DOI: https://doi.org/10.2210/pdb1WBI/pdb

Classification: AVIDIN-RELATED PROTEIN
Organism(s): Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-11-01 Released: 2005-10-12
Deposition Author(s): Airenne, T.T., Hytonen, V.P., Maatta, J.H., Kidron, H., Halling, K.K., Horha, J., Kulomaa, T., Nyholm, T.K.M., Johnson, M.S., Salminen, T.A., Kulomaa, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.201
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Avidin Related Protein 2 Shows Unique Structural and Functional Features Among the Avidin Protein Family.

Hytonen, V.P., Maatta, J.A., Kidron, H., Halling, K.K., Horha, J., Kulomaa, T., Nyholm, T.K.M., Johnson, M.S., Salminen, T.A., Kulomaa, M.S., Airenne, T.T.

(2005) BMC Biotechnol 5: 28

PubMed: 16212654 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6750-5-28
Primary Citation of Related Structures:
1WBI

PubMed Abstract:
The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin.

Organizational Affiliation

NanoScience Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (YAB), FI-40014, Finland. veshyto@bytl.jyu.fi

Macromolecule Content

Total Structure Weight: 118.43 kDa
Atom Count: 9,122
Modelled Residue Count: 970
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AVIDIN-RELATED PROTEIN 2	A, B, C, D, E A, B, C, D, E, F, G, H	129	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P56732 (Gallus gallus) Explore P56732 Go to UniProtKB: P56732
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN Query on BTN Download Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	EA [auth G] HA [auth H] I [auth A] N [auth B] R [auth C] EA [auth G], HA [auth H], I [auth A], N [auth B], R [auth C], V [auth D], W [auth E], Z [auth F]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain EA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain EA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Z [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	CA [auth F] DA [auth F] FA [auth G] GA [auth G] IA [auth H] CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], K [auth A], L [auth A], M [auth A], Q [auth B], T [auth C], U [auth C], X [auth E], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth E] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C]	AA [auth F] BA [auth F] J [auth A] O [auth B] P [auth B] AA [auth F], BA [auth F], J [auth A], O [auth B], P [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.201
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.669	α = 90
b = 99.936	β = 90
c = 135.191	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-10-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-12
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description