2BEH
Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin
- PDB DOI: https://doi.org/10.2210/pdb2BEH/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Expression System: Mesocricetus auratus
- Mutation(s): Yes 
- Deposited: 2005-10-24 Released: 2005-11-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.265 
- R-Value Work: 0.219 
- R-Value Observed: 0.219 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Antithrombin-III | A [auth I] | 432 | Homo sapiens | Mutation(s): 3  Gene Names: SERPINC1, AT3 | |
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], E [auth C] | 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D [auth B] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth I], H [auth L] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | G [auth I] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.265 
- R-Value Work: 0.219 
- R-Value Observed: 0.219 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 68.073 | α = 90 |
b = 97.274 | β = 105.03 |
c = 87.388 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2005-11-01  Deposition Author(s): Johnson, D.J., Luis, S.A., Huntington, J.A.
Revision History (Full details and data files)
- Version 1.0: 2005-11-01
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - 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: 2021-10-20
Changes: Database references, Structure summary