2A5C
Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine
- PDB DOI: https://doi.org/10.2210/pdb2A5C/pdb
- Classification: UNKNOWN FUNCTION
- Organism(s): Gallus gallus
- Mutation(s): Yes 
- Deposited: 2005-06-30 Released: 2006-05-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.308 
- R-Value Work: 0.221 
- R-Value Observed: 0.225 
This is version 1.5 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Avidin | 123 | Gallus gallus | Mutation(s): 1  | ||
UniProt | |||||
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02701 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
8DA Query on 8DA | D [auth A], F [auth B] | 8-OXODEOXYADENOSINE C10 H15 N5 O4 KTCVXRUKSBTHOG-SRQIZXRXSA-N | |||
NAG Query on NAG | C [auth A], E [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.308 
- R-Value Work: 0.221 
- R-Value Observed: 0.225 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 70.584 | α = 90 |
b = 79.052 | β = 90 |
c = 42.997 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2006-05-23  Deposition Author(s): Conners, R., Hooley, E., Thomas, S., Brady, R.L.
Revision History (Full details and data files)
- Version 1.0: 2006-05-23
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: 2017-10-11
Changes: Advisory, Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.5: 2023-08-23
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary