5IRW
Crystal structure of avidin in complex with 1-desthiobiotinylpyrene
- PDB DOI: https://doi.org/10.2210/pdb5IRW/pdb
- Classification: biotin binding protein
- Organism(s): Gallus gallus
- Mutation(s): No
- Deposited: 2016-03-14 Released: 2016-10-12
- Funding Organization(s): National Science Centre
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.231
- R-Value Work: 0.195
- R-Value Observed: 0.197
This is version 1.4 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 | 128 | Gallus gallus | Mutation(s): 0 |  | |
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 | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D9P Query on D9P | F [auth A], H [auth B], J [auth C], L [auth D] | 1-desthiobiotinylpyrene C26 H26 N2 O2 GEJQOLRONNVYHQ-KSFYIVLOSA-N |  | ||
| NAG Query on NAG | E [auth A], G [auth B], I [auth C], K [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.231
- R-Value Work: 0.195
- R-Value Observed: 0.197
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.97 | α = 90 |
| b = 81.52 | β = 90 |
| c = 107.78 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-10-12 Deposition Author(s): Strzelczyk, P., Bujacz, G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Centre | Poland | DEC-2013/11/N/ST5/01296 |
| National Science Centre | Poland | DEC-2015/16/T/ST5/00401 |
Revision History (Full details and data files)
- Version 1.0: 2016-10-12
Type: Initial release - Version 1.1: 2016-10-19
Changes: Database references - Version 1.2: 2018-03-07
Changes: Data collection - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
