2DPI Transferase Dna date May 12, 2006
title Ternary Complex Of Hpoli With Dna And Dctp
authors D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal
compound source
Molecule: 5'-D(Apgpgpapcpcp(Doc))-3'
Chain: P
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tp(Eda)Pgpgpgptpcpcpt)-3'
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iota
Chain: A
Fragment: Residues 1-420
Synonym: Rad30 Homolog B, Eta2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rad30 Homolog B, Eta2
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
Expression_system_strain: Bj5464
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbj941
symmetry Space Group: P 65 2 2
R_factor 0.228 R_Free 0.278
length a length b length c angle alpha angle beta angle gamma
98.148 98.148 203.112 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand DCP, DOC, EDA, MG enzyme Transferase E.C. BRENDA

Primary referenceHoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Nat Struct Mol Biol. 2006 Jul;13(7):619-25. Epub 2006 Jul 2. PMID:16819516
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2dpi.pdb1.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 2DPI
  • CSU: Contacts of Structural Units for 2DPI
  • Likely Quarternary Molecular Structure file(s) for 2DPI
  • Structure Factors (159 Kb)
  • Retrieve 2DPI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DPI from S2C, [Save to disk]
  • Re-refined 2dpi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DPI 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 2DPI
  • 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 2DPI, from MSDmotif at EBI
  • Fold representative 2dpi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dpi_A] [2dpi_P] [2dpi] [2dpi_T]
  • SWISS-PROT database: [Q9UNA4]
  • Domain organization of [POLI_HUMAN] by SWISSPFAM
  • Other resources with information on 2DPI
  • Community annotation for 2DPI 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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