3EDX

Crystal structure of the W215A/E217A mutant of murine thrombin


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chain
A, C, E
44Mus musculusMutation(s): 0 
Gene Names: F2Cf2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19221
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chain
B, D, F
258Mus musculusMutation(s): 2 
Gene Names: F2Cf2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19221
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
J [auth D]
K [auth D]
L [auth D]
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 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.716α = 90
b = 105.76β = 90
c = 176.811γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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