3M6Z

Crystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride

Structural Biology Knowledgebase: 3M6Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 3M6Z

Classification: ISOMERASE

Total Structure Weight: 89450.78

Macromolecule Entities
Molecule Chains Length Organism Details
Topoisomerase V A, B 380 Methanopyrus kandleri Fragment: N-terminal 44 kDa fragment (Topo-44)
Gene Name(s): top5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAI
Query on GAI

A, B GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.4 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.165
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.64 α = 90.00
b = 80.11 β = 90.00
c = 137.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-16
  • Released Date: 2010-08-04
  • Deposition author(s): Rajan, R., Taneja, B., Mondragon, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4