1KDH

Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA

Structural Biology Knowledgebase: 1KDH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.297
  • R-Value Work: 0.239

Literature

Macromolecules
Sequence Display for 1KDH

Classification: TRANSFERASE / DNA

Total Structure Weight: 43394.79


Macromolecule Entities
Molecule Chains Length Organism Details
Terminal deoxynucleotidyltransferase short isoform A 363 Mus musculus EC#: 2.7.7.31 IUBMB
Gene Name(s): Dntt Tdt
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3' D 4 synthetic

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

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
D DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.297
  • R-Value Work: 0.239
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.80 α = 90.00
b = 85.00 β = 90.00
c = 111.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-13
  • Released Date: 2002-05-13
  • Deposition author(s): Delarue, M., Boule, J.B., Lescar, J., Expert-Bezancon, N., Jourdan, N., Sukumar, N., Rougeon, F., Papanicolaou, C.

Revision History

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