2ORV

human Thymidine Kinase 1 in complex with TP4A

Structural Biology Knowledgebase: 2ORV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 2ORV

Classification: TRANSFERASE

Total Structure Weight: 52512.89

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidine kinase A, B 234 Homo sapiens EC#: 2.7.1.21 IUBMB
Mutation: K203A, E204A
Gene Name(s): TK1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4TA
Query on 4TA

A, B P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
C20 H25 N7 O20 P4
WLGHSSFVEUABFP-SLFMBYJQSA-J
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4TA N/A in BindingDB
Kd: 29 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.197
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.98 α = 90.00
b = 80.98 β = 90.00
c = 156.36 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-04
  • Released Date: 2007-03-27
  • Deposition author(s): Segura-Pena, D., Lutz, S., Monnerjahn, C., Konrad, M., Lavie, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values