3QX3

Human topoisomerase IIbeta in complex with DNA and etoposide

Structural Biology Knowledgebase: 3QX3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QX3

Classification: ISOMERASE / DNA / ISOMERASE INHIBITOR

Total Structure Weight: 197363.46


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 2-beta A, B 803 Homo sapiens EC#: 5.99.1.3 IUBMB
Fragment: hTOP2beta cleavage core, UNP residues 450-1206
Gene Name(s): TOP2B Gene View
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') C, E 8 synthetic
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') D, F 12 synthetic

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

A, D (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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, D, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EVP EC50: >70000 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.168
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 80.15 α = 90.00
b = 176.80 β = 111.58
c = 94.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-01
  • Released Date: 2011-07-06
  • Deposition author(s): Wu, C.C., Li, T.K., Farh, L., Lin, L.Y., Lin, T.S., Yu, Y.J., Yen, T.J., Chiang, C.W., Chan, N.L.

Revision History

  • 2012-01-25
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4