1E2D

HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION

Structural Biology Knowledgebase: 1E2D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1E2D

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 24875.05

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE KINASE A 215 Homo sapiens EC#: 2.7.4.9 IUBMB
Mutation: R200A, R183S, L184I, E190D, L191I
Gene Name(s): DTYMK Gene View CDC8 TMPK TYMK

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

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

A THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.201
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.00 α = 90.00
b = 101.00 β = 90.00
c = 49.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-05-22
  • Released Date: 2001-05-17
  • Deposition author(s): Ostermann, N., Schlichting, I., Brundiers, R., Konrad, M., Reinstein, J., Veit, T., Goody, R.S., Lavie, A.

Revision History

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