3G6Y Replication Dna date Feb 09, 2009
title Ternary Complex Of Dna Polymerase Iota:Dna:Dttp With An Abas The Templating Position
authors D.T.Nair, A.K.Aggarwal
compound source
Molecule: Dna Polymerase Iota
Chain: A
Synonym: Rad30 Homolog B, Eta2
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poli, Rad30b
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Bj5464
Expression_system_vector: Plasmid
Expression_system_plasmid: Pbj941

Molecule: Primer Dna Strand
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Oligonucleotide Synthesis

Molecule: Template Dna Strand
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Oligonucleotide Synthesis
symmetry Space Group: P 65 2 2
R_factor 0.220 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.114 98.114 202.823 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand 3DR, DOC, MG, TTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Structure. 2009 Apr 15;17(4):530-7. PMID:19368886
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (3g6y.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3G6Y
  • CSU: Contacts of Structural Units for 3G6Y
  • Likely Quarternary Molecular Structure file(s) for 3G6Y
  • Structure Factors (251 Kb)
  • Retrieve 3G6Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G6Y from S2C, [Save to disk]
  • Re-refined 3g6y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G6Y 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 3G6Y
  • 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
  • 3D motif for 3G6Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g6y_T] [3g6y_P] [3g6y_A] [3g6y]
  • SWISS-PROT database: [Q9UNA4]
  • Domain organization of [POLI_HUMAN] by SWISSPFAM
  • Other resources with information on 3G6Y
  • Community annotation for 3G6Y 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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