1NN5

Crystal structure of human thymidylate kinase with d4TMP + AppNHp

Structural Biology Knowledgebase: 1NN5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1NN5

Classification: TRANSFERASE

Total Structure Weight: 24913.74

Macromolecule Entities
Molecule Chains Length Organism Details
Similar to deoxythymidylate kinase (thymidylate kinase) A 215 Homo sapiens EC#: 2.7.4.9 IUBMB
Mutation: R200A
Gene Name(s): DTYMK Gene View CDC8 TMPK TYMK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2DT
Query on 2DT

A 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE (Synonym)
C10 H15 N2 O7 P
WVNRRNJFRREKAR-JGVFFNPUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.192
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.10 α = 90.00
b = 101.10 β = 90.00
c = 49.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-12
  • Released Date: 2003-03-18
  • Deposition author(s): Ostermann, N., Segura-Pena, D., Meier, C., Veit, T., Monnerjahn, M., 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