1K4T

HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 1K4T

Classification: ISOMERASE / DNA

Total Structure Weight: 84971.68


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase I A 592 Homo sapiens EC#: 5.99.1.2 IUBMB
Fragment: Core Domain and C-Terminal Domain, Residues 174-765
Mutation: Y723X
Gene Name(s): TOP1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' B 10 synthetic
5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' C 12 synthetic
5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' D 22 synthetic

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

C 2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL- 9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN- 7-YL)-2-HYDROXY-BUTYRIC ACID
HYDROLYZED PRODUCT OF TOPOTECAN (Synonym)
C23 H25 N3 O6
DPQJTQJZJNYUEC-QHCPKHFHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TTC
Query on TTC

D (S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9- DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2- B]-QUINOLINE-3,14(4H,12H)-DIONE
TOPOTECAN, HYCAMTIN (Synonym)
C23 H23 N3 O5
UCFGDBYHRUNTLO-QHCPKHFHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

A MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TTC IC50: 20000 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
TGP
Query on TGP
C DNA LINKING C10 H14 N5 O6 P S DG
PTR
Query on PTR
A L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.229
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 57.09 α = 90.00
b = 116.26 β = 94.16
c = 75.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-08
  • Released Date: 2002-12-04
  • Deposition author(s): Staker, B.L., Hjerrild, K., Feese, M.D., Behnke, C.A., Burgin Jr., A.B., Stewart, L.J.

Revision History

  • Version 1_0: 2002-12-04

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance