2A30

Crystal structure of human deoxycytidine kinase in complex with deoxycytidine

Structural Biology Knowledgebase: 2A30 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2A30

Classification: TRANSFERASE

Total Structure Weight: 117545.97

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxycytidine kinase A, B, C, D 248 Homo sapiens EC#: 2.7.1.74 IUBMB
Mutation: ΔQ65, ΔD66, ΔE67, ΔF68, ΔE69, ΔE70, ΔL71, ΔT72, ΔM73, ΔS74, ΔQ75, ΔK76, ΔN77, ΔG78, ΔG79
Gene Name(s): DCK Gene View

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

A, B, C, D 2'-DEOXYCYTIDINE
C9 H13 N3 O4
CKTSBUTUHBMZGZ-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.235
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 79.34 α = 90.00
b = 64.94 β = 95.97
c = 108.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-06-23
  • Released Date: 2006-01-17
  • Deposition author(s): Godsey, M.H., Ort, S., Sabini, E., Konrad, M., Lavie, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4