3IAY Transferase Dna date Jul 15, 2009
title Ternary Complex Of Dna Polymerase Delta
authors M.K.Swan, A.K.Aggarwal
compound source
Molecule: 5'-D(Aptpcpcptpcpcpcpcptpap(Doc))-3'
Chain: P
Engineered: Yes
Synthetic: Yes
Other_details: Oligonucleotide Synthesis

Molecule: 5'-D(Tpapapgpgptpapgpgpgpgpapgpgpa
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Oligonucleotide Synthesis

Molecule: Dna Polymerase Delta Catalytic Subunit
Chain: A
Fragment: Unp Residues 67 To 985
Synonym: Dna Polymerase III
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Gene: Pol3
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
symmetry Space Group: P 1 21 1
R_factor 0.193 R_Free 0.236
length a length b length c angle alpha angle beta angle gamma
81.077 85.948 86.872 90.00 111.10 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ACT, CA, DCP, DOC enzyme Transferase E.C. BRENDA

Primary referenceStructural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta., Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Nat Struct Mol Biol. 2009 Sep;16(9):979-86. Epub 2009 Aug 30. PMID:19718023
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (3iay.pdb1.gz) 164 Kb
  • LPC: Ligand-Protein Contacts for 3IAY
  • CSU: Contacts of Structural Units for 3IAY
  • Structure Factors (688 Kb)
  • Retrieve 3IAY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IAY from S2C, [Save to disk]
  • Re-refined 3iay structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IAY 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 3IAY
  • 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 3IAY, from MSDmotif at EBI
  • Fold representative 3iay from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iay] [3iay_A] [3iay_T] [3iay_P]
  • SWISS-PROT database: [P15436]
  • Domain organization of [DPOD_YEAST] by SWISSPFAM
  • Domain found in 3IAY: [POLBc ] by SMART
  • Other resources with information on 3IAY
  • Community annotation for 3IAY 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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