5INL

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with deoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.129

Literature

Macromolecules
Sequence Display for 5INL

Classification: hydrolase / dna

Total Structure Weight: 63707.45


Macromolecule Entities
Molecule Chains Length Organism Details
Tyrosyl-DNA phosphodiesterase 2 A, B 256 Mus musculus EC#: 3.1.4 IUBMB
Fragment: unp residues 118-370
Gene Name(s): Tdp2 Ttrap
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3') C, D 9 Homo sapiens

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

B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.129
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.90 α = 90.00
b = 69.05 β = 90.00
c = 167.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-03-07
  • Released Date: 2016-04-27
  • Deposition author(s): Schellenberg, M.J., Vilas, C.K., Williams, R.S.

Revision History

  • Version 1_0: 2016-04-27

    Type: Initial release

  • Version 1_1: 2016-05-18

    Type: Database references

  • Version 1_2: 2017-09-20

    Type: Author supporting evidence, Database references, Derived calculations