3EDX
Crystal structure of the W215A/E217A mutant of murine thrombin
- PDB DOI: https://doi.org/10.2210/pdb3EDX/pdb
- Classification: HYDROLASE
- Organism(s): Mus musculus
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2008-09-03 Released: 2009-07-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.243 
- R-Value Work: 0.214 
- R-Value Observed: 0.214 
This is version 1.4 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 light chain | 44 | Mus musculus | Mutation(s): 0  Gene Names: F2, Cf2 EC: 3.4.21.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P19221 (Mus musculus) Explore P19221  Go to UniProtKB:  P19221 | |||||
IMPC:  MGI:88380 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P19221 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin heavy chain | 258 | Mus musculus | Mutation(s): 2  Gene Names: F2, Cf2 EC: 3.4.21.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P19221 (Mus musculus) Explore P19221  Go to UniProtKB:  P19221 | |||||
IMPC:  MGI:88380 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P19221 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth B], M [auth D], P [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | G [auth B] H [auth B] J [auth D] K [auth D] L [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.243 
- R-Value Work: 0.214 
- R-Value Observed: 0.214 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 97.716 | α = 90 |
b = 105.76 | β = 90 |
c = 176.811 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-07-07  Deposition Author(s): Gandhi, P.S., Page, M.J., Chen, Z., Bush-pelc, L., Di Cera, E.
Revision History (Full details and data files)
- Version 1.0: 2009-07-07
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2021-10-20
Changes: Database references, Structure summary - Version 1.4: 2023-08-30
Changes: Data collection, Refinement description