1P62

Structure of human dCK complexed with gemcitabine and ADP-MG

Structural Biology Knowledgebase: 1P62 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1P62

Classification: TRANSFERASE

Total Structure Weight: 31549.71

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxycytidine kinase B 263 Mus musculus EC#: 2.7.1.74 IUBMB
Gene Name(s): DCK Gene View

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

B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GEO
Query on GEO

B GEMCITABINE
2',2'-DIFLUORODEOXYCYTIDINE (Synonym)
C9 H11 F2 N3 O4
SDUQYLNIPVEERB-QPPQHZFASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.179
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.20 α = 90.00
b = 81.20 β = 90.00
c = 94.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-28
  • Released Date: 2003-07-01
  • Deposition author(s): Sabini, E., Ort, S., Monnerjahn, C., Konrad, M., Lavie, A.

Revision History

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