1NH3 Isomerase Dna date Dec 18, 2002
title Human Topoisomerase I Ara-C Complex
authors J.E.Chrencik, A.B.Burgin, Y.Pommier, L.Stewart, M.R.Redinbo
compound source
Molecule: 5'-D(Apapapapapgpapcpup(Ubb))-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D((Gng)Pgpapapapapapupupupupt)-3'
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Apapapapaptpupupupupcp(Car) Papapgpupcpupupupupt)-3';
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Dna Topoisomerase I
Chain: A
Fragment: Core Subdomain, C-Terminal Domain
Ec: 5.99.1.2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Top1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 32
R_factor 0.235 R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.970 72.970 186.290 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand CAR, GNG, PTR, UBB enzyme Isomerase E.C.5.99.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural impact of the leukemia drug 1-beta-D-arabinofuranosylcytosine (Ara-C) on the covalent human topoisomerase I-DNA complex., Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo MR, J Biol Chem 2003 Apr 4;278(14):12461-6. Epub 2003 Jan 17. PMID:12533542
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (1nh3.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 1NH3
  • CSU: Contacts of Structural Units for 1NH3
  • Likely Quarternary Molecular Structure file(s) for 1NH3
  • Structure Factors (299 Kb)
  • Retrieve 1NH3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NH3 from S2C, [Save to disk]
  • Re-refined 1nh3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NH3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1NH3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NH3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nh3a2, region A:203-430 [Jmol] [rasmolscript] [script source]
        - Domain d1nh3a1, region A:431-626,A:719-765 [Jmol] [rasmolscript] [script source]
  • Fold representative 1nh3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nh3_D] [1nh3] [1nh3_B] [1nh3_A] [1nh3_C]
  • SWISS-PROT database: [P11387]
  • Domain organization of [TOP1_HUMAN] by SWISSPFAM
  • Domain found in 1NH3: [TOPEUc ] by SMART
  • Other resources with information on 1NH3
  • Community annotation for 1NH3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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