3IN5 Transferase Dna date Aug 11, 2009
title Structure Of Human Dna Polymerase Kappa Inserting Datp Opposite An 8-Oxog Dna Lesion
authors T.D.Silverstein, R.Vasquez-Del Carpio, A.K.Aggarwal
compound source
Molecule: Dna Polymerase Kappa
Chain: A, B
Fragment: Unp Residues 19-526
Synonym: Dinb Protein, Dinp
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dinb1, Polk
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Bj5464
Expression_system_vector_type: Plasmid

Molecule: Dna (5'- D(Gpggpgpgpapapgpgpapcptp(Doc))-3');
Chain: P, Q
Engineered: Yes
Other_details: Dna Primer Strand

Synthetic: Yes

Molecule: Dna (5'-D(Ccptpap(8og) Pgpapgptpcpcptptpcpcpcpcpc)-3');
Chain: T, U
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.846 154.480 217.293 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand 8OG, ATP, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
note 3IN5 supersedes 3HED
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion., Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan MK, Choudhury JR, Johnson RE, Prakash S, Prakash L, Aggarwal AK, PLoS One. 2009 Jun 2;4(6):e5766. PMID:19492058
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (3in5.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (3in5.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3IN5
  • CSU: Contacts of Structural Units for 3IN5
  • Structure Factors (516 Kb)
  • Retrieve 3IN5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IN5 from S2C, [Save to disk]
  • Re-refined 3in5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IN5 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 3IN5
  • 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 3IN5, from MSDmotif at EBI
  • Fold representative 3in5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3in5_B] [3in5_A] [3in5_U] [3in5_P] [3in5_T] [3in5] [3in5_Q]
  • SWISS-PROT database: [Q9UBT6]
  • Domain organization of [POLK_HUMAN] by SWISSPFAM
  • Other resources with information on 3IN5
  • Community annotation for 3IN5 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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