2ODY
Thrombin-bound boophilin displays a functional and accessible reactive-site loop
- PDB DOI: https://doi.org/10.2210/pdb2ODY/pdb
- Classification: BLOOD CLOTTING/BLOOD CLOTTING INHIBITOR
- Organism(s): Bos taurus, Rhipicephalus microplus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-12-27 Released: 2008-01-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.230
- R-Value Work: 0.190
- R-Value Observed: 0.192
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 |
| Prothrombin (EC 3.4.21.5) | 49 | Bos taurus | Mutation(s): 0 EC: 3.4.21.5 |  | |
UniProt | |||||
Find proteins for P00735 (Bos taurus) Explore P00735 Go to UniProtKB: P00735 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00735 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Prothrombin (EC 3.4.21.5) | 259 | Bos taurus | Mutation(s): 0 EC: 3.4.21.5 |  | |
UniProt | |||||
Find proteins for P00735 (Bos taurus) Explore P00735 Go to UniProtKB: P00735 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00735 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Boophilin | 127 | Rhipicephalus microplus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q8WPI2 (Rhipicephalus microplus) Explore Q8WPI2 Go to UniProtKB: Q8WPI2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8WPI2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | K [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| PO4 Query on PO4 | G [auth A], H [auth B], I [auth B], M [auth F] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| NA Query on NA | J [auth B], L [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.230
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 92.5 | α = 90 |
| b = 104.2 | β = 90 |
| c = 129.1 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2008-01-22 Deposition Author(s): Macedo-Ribeiro, S., Fuentes-Prior, P., Pereira, P.J.B.
Revision History (Full details and data files)
- Version 1.0: 2008-01-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.3: 2023-08-30
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
