3EDX | pdb_00003edx

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 
• Deposition Author(s): Gandhi, P.S., Page, M.J., Chen, Z., Bush-pelc, L., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis for the Kinetic Differences of the W215A/E217A Mutant of Human and Murine Thrombin

Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.04 kDa 
• Atom Count: 7,612 
• Modeled Residue Count: 900 
• Deposited Residue Count: 906 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A, C, E	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B, D, F	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P19221-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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	G [auth B], H [auth B], J [auth D], K [auth D], L [auth D], N [auth F], O [auth F]	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 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

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 Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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  

• 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
• Version 1.5: 2024-11-06
  Changes: Structure summary