1CY8

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE

Structural Biology Knowledgebase: 1CY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 1CY8

Classification: ISOMERASE

Total Structure Weight: 68282.57

Macromolecule Entities
Molecule Chains Length Organism Details
DNA TOPOISOMERASE I A 599 Escherichia coli EC#: 5.99.1.2 IUBMB
Fragment: 67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Gene Name(s): topA supX b1274 JW1266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
T3P
Query on T3P

A THYMIDINE-3'-PHOSPHATE
ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE (Synonym)
C10 H15 N2 O8 P
XXYIANZGUOSQHY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 63.61 α = 90.00
b = 79.27 β = 90.00
c = 141.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-08-31
  • Released Date: 2000-03-08
  • Deposition author(s): Feinberg, H., Changela, A., Mondragon, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name