1SG8
Crystal structure of the procoagulant fast form of thrombin
- PDB DOI: https://doi.org/10.2210/pdb1SG8/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2004-02-23 Released: 2004-06-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.289 
- R-Value Work: 0.219 
- R-Value Observed: 0.219 
This is version 1.5 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 |
thrombin | A, C [auth D] | 36 | Homo sapiens | Mutation(s): 0  Gene Names: F2 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
thrombin | B, D [auth E] | 259 | Homo sapiens | Mutation(s): 1  Gene Names: F2 EC: 3.4.21.5 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth B], G [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
NA Query on NA | F [auth B], H [auth E] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.289 
- R-Value Work: 0.219 
- R-Value Observed: 0.219 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.49 | α = 90 |
b = 65.58 | β = 90 |
c = 162.44 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2004-06-08  Deposition Author(s): Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S., Di Cera, E.
Revision History (Full details and data files)
- Version 1.0: 2004-06-08
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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2021-10-27
Changes: Database references, Structure summary - Version 1.5: 2023-08-23
Changes: Data collection, Refinement description