1NOP

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

Structural Biology Knowledgebase: 1NOP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1NOP

Classification: HYDROLASE / DNA

Total Structure Weight: 114410.20


Macromolecule Entities
Molecule Chains Length Organism Details
tyrosyl-DNA phosphodiesterase 1 A, B 485 Homo sapiens EC#: 3.1.4 IUBMB
Fragment: residues 149-608
Mutation: D322N, M328T, F548L
Gene Name(s): TDP1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
topoisomerase I-derived peptide C 8 synthetic Fragment: residues 720-727
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*GP*AP*GP*TP*T)-3' D, F 6 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VO4
Query on VO4

A, B VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.206
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.80 α = 90.00
b = 104.72 β = 90.00
c = 193.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-16
  • Released Date: 2003-03-11
  • Deposition author(s): Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.J.

Revision History

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