1OYH
Crystal Structure of P13 Alanine Variant of Antithrombin
- PDB DOI: https://doi.org/10.2210/pdb1OYH/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes
- Deposited: 2003-04-04 Released: 2004-04-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.258
- R-Value Work: 0.221
This is version 2.2 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 |
| Antithrombin-III | A [auth I] | 432 | Homo sapiens | Mutation(s): 2 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01008 (Homo sapiens) Explore P01008 Go to UniProtKB: P01008 | |||||
PHAROS: P01008 GTEx: ENSG00000117601 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01008 | ||||
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 |
| Antithrombin-III | B [auth L] | 432 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01008 (Homo sapiens) Explore P01008 Go to UniProtKB: P01008 | |||||
PHAROS: P01008 GTEx: ENSG00000117601 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01008 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A], D [auth B] | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C] | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | F [auth I], G [auth I], H [auth L], I [auth L] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.258
- R-Value Work: 0.221
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.998 | α = 90 |
| b = 98.573 | β = 105.53 |
| c = 89.35 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345 | data collection |
| SCALA | data scaling |
| MOLREP | phasing |
| CNS | refinement |
| CCP4 | data scaling |
Entry History
Deposition Data
- Released Date: 2004-04-13 Deposition Author(s): Johnson, D.J.D., Huntington, J.A.
Revision History (Full details and data files)
- Version 1.0: 2004-04-13
Type: Initial release - Version 1.1: 2008-04-29
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2021-10-27
Changes: Database references, Structure summary - Version 2.2: 2023-08-16
Changes: Data collection, Refinement description
