1RG2

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 1RG2

Classification: HYDROLASE / DNA

Total Structure Weight: 112937.03


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
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*GP*TP*A)-3' D, F 4 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SPM
Query on SPM

A SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OTR
Query on OTR

A, B 4-(2R-AMINO-1-HYDROXYETHYL)PHENOL
R-OCTOPAMINE (Synonym)
C8 H11 N O2
QHGUCRYDKWKLMG-QMMMGPOBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OTS
Query on OTS

A, B 4-(2S-AMINO-1-HYDROXYETHYL)PHENOL
S-OCTOPAMINE (Synonym)
C8 H11 N O2
QHGUCRYDKWKLMG-MRVPVSSYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.195
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 49.81 α = 90.00
b = 104.69 β = 90.00
c = 193.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-11-11
  • Released Date: 2004-03-02
  • Deposition author(s): Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.

Revision History

  • Version 1_0: 2004-03-02

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance