3GV5 Transferase Dna date Mar 30, 2009
title Human Dna Polymerase Iota In Complex With T Template Dna And Ddadp
authors K.N.Kirouac, H.Ling
compound source
Molecule: Dna Polymerase Iota
Chain: B, D
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: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parrallel1

Molecule: 5'-D(Gptpgpgpaptpgpapg)-3'
Chain: P, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Pcpaptptpcptpcpaptpcpcpapc)-3'
Chain: T, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.205 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
140.160 71.750 127.420 90.00 112.53 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ADI, CA, GOL, MSE enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
D, B


Primary referenceStructural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota., Kirouac KN, Ling H, EMBO J. 2009 May 14. PMID:19440206
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (3gv5.pdb1.gz) 80 Kb
  • Biological Unit Coordinates (3gv5.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3GV5
  • CSU: Contacts of Structural Units for 3GV5
  • Likely Quarternary Molecular Structure file(s) for 3GV5
  • Structure Factors (600 Kb)
  • Retrieve 3GV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GV5 from S2C, [Save to disk]
  • Re-refined 3gv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GV5 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 3GV5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3GV5, from MSDmotif at EBI
  • Fold representative 3gv5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gv5_P] [3gv5_F] [3gv5_E] [3gv5] [3gv5_B] [3gv5_T] [3gv5_D]
  • SWISS-PROT database: [Q9UNA4]
  • Domain organization of [POLI_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3GV5 with the sequences similar proteins can be viewed for 3GV5's classification [POLI_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [POLI_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3GV5
  • Community annotation for 3GV5 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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