5GWK

Human topoisomerase IIalpha in complex with DNA and etoposide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 5GWK

Classification: ISOMERASE / DNA / ISOMERASE INHIBITOR

Total Structure Weight: 199340.44


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2-alpha A, B 806 Homo sapiens EC#: 5.99.1.3 IUBMB
Fragment: UNP residues 430-1188
Gene Name(s): TOP2A Gene View TOP2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') C, E 8 Synthetic construct
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') D, F 12 Synthetic construct

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

D, F (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)- 8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3- d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]- beta-D-glucopyranoside
Etoposide; VP-16 (Synonym)
C29 H32 O13
VJJPUSNTGOMMGY-MRVIYFEKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, D, F 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: 3.15 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.203
  • Space Group: P 21 2 21

Unit Cell:

Length (Å) Angle (°)
a = 105.11 α = 90.00
b = 126.15 β = 90.00
c = 198.86 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-09-12
  • Released Date: 2017-08-23
  • Deposition author(s): Wang, Y.R., Wu, C.C., Chan, N.L.

Revision History

No revisions since initial release