1S0M Transferase Dna date Dec 31, 2003
title Crystal Structure Of A Benzo[A]Pyrene Diol Epoxide Adduct In Complex With A Dna Polymerase
authors H.Ling, J.M.Sayer, F.Boudsocq, B.S.Plosky, R.Woodgate, W.Yang
compound source
Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpt)-3'
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Paptpapapaptpcpcptptpcpcpcpcp
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Gene: Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.029 103.545 106.127 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand BAP, CA, DTP, MG enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1N56, 1S0N
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase., Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F, Woodgate R, Jerina DM, Yang W, Proc Natl Acad Sci U S A 2004 Feb 24;101(8):2265-9. PMID:14982998
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (1s0m.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (1s0m.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 1S0M
  • CSU: Contacts of Structural Units for 1S0M
  • Likely Quarternary Molecular Structure file(s) for 1S0M
  • Structure Factors (279 Kb)
  • Retrieve 1S0M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S0M from S2C, [Save to disk]
  • Re-refined 1s0m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1S0M 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 1S0M
  • 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 1S0M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s0ma2, region A:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s0ma1, region A:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1s0mb2, region B:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s0mb1, region B:241-341 [Jmol] [rasmolscript] [script source]
  • Fold representative 1s0m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s0m_C] [1s0m_E] [1s0m_F] [1s0m_D] [1s0m_B] [1s0m] [1s0m_A]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 1S0M
  • Community annotation for 1S0M 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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