5TVP

SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 5TVP

Classification: hydrolase / dna

Total Structure Weight: 264101.72


Macromolecule Entities
Molecule Chains Length Organism Details
Tyrosyl-DNA phosphodiesterase 2 A, B, E..., G, I, K, M, OA, B, E, G, I, K, M, O 256 Mus musculus EC#: 3.1.4 IUBMB
Gene Name(s): Tdp2 Ttrap
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small ubiquitin-related modifier 2 Q 81 Mus musculus Gene Name(s): Sumo2 Smt3b Smt3h2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') C, D, F... , H, J, L, N, P C, D, F, H, J, L, N, P 9 Homo sapiens

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B, E, G, I, K, M, O PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, G, I, K, O 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B, E, M CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.191
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 106.55 α = 90.00
b = 113.77 β = 91.52
c = 125.43 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-11-09
  • Released Date: 2017-10-11
  • Deposition author(s): Schellenberg, M.J., Williams, R.S.

Revision History

  • Version 1_0: 2017-10-11

    Type: Initial release