5HLM
Crystal structure of avidin complex with a ferrocene biotin derivative
- PDB DOI: https://doi.org/10.2210/pdb5HLM/pdb
- Classification: BIOTIN-BINDING PROTEIN
- Organism(s): Gallus gallus
- Mutation(s): No
- Deposited: 2016-01-15 Released: 2017-01-18
- Funding Organization(s): National Science Centre
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.254
- R-Value Work: 0.202
- R-Value Observed: 0.204
This is version 1.3 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 | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| B9F Query on B9F | E [auth A], G [auth B], I [auth C], K [auth D] | [(1,2,3,4,5-eta)-cyclopentadienyl]{(1,2,3,4,5-eta)-1-[1-hydroxy-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentyl]cyclopentadienyl}iron C20 H26 Fe N2 O2 S ZYEYPNBFMRLUKC-MIZLAOAMSA-N |  | ||
| NAG Query on NAG | F [auth A], H [auth B], J [auth C], L [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: 2.50 Å
- R-Value Free: 0.254
- R-Value Work: 0.202
- R-Value Observed: 0.204
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 43.2 | α = 90 |
| b = 74.91 | β = 106.17 |
| c = 76.18 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-01-18 Deposition Author(s): Strzelczyk, P., Bujacz, G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Centre | Poland | DEC-2013/11/N/ST5/01296 |
Revision History (Full details and data files)
- Version 1.0: 2017-01-18
Type: Initial release - Version 1.1: 2018-03-07
Changes: Data collection - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
