3T5L Dna Transferase date Jul 27, 2011
title Ternary Complex Of Hne Adduct Modified Dna (5'-Cxg-3' Vs 14- Dpo4 And Incoming Ddgt
authors S.Banerjee, P.P.Christov, A.Kozekova, C.J.Rizzo, M.P.Stone
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus P2
Organism_taxid: 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpapcp(Hn0) Pgpapaptpcpcptptpcpcpcpcpc)-3');
Chain: B
Engineered: Yes
Other_details: Modified Dna Template

Synthetic: Yes
Other_details: Synthetic Construct

Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpaptptpcp
Chain: C
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 21 21 2
R_factor 0.204 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
95.124 103.716 52.816 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, DGT, HN0 enzyme Transferase E.C. BRENDA

Primary referenceReplication Bypass of the trans-4-Hydroxynonenal-Derived (6S,8R,11S)-1,N(2)-Deoxyguanosine DNA Adduct by the Sulfolobus solfataricus DNA Polymerase IV., Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP, Chem Res Toxicol. 2012 Feb 7. PMID:22313351
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3t5l.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3T5L
  • CSU: Contacts of Structural Units for 3T5L
  • Structure Factors (166 Kb)
  • Retrieve 3T5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3T5L from S2C, [Save to disk]
  • Re-refined 3t5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3T5L in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3T5L
  • 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 3T5L, from MSDmotif at EBI
  • Fold representative 3t5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3t5l_A] [3t5l_B] [3t5l_C] [3t5l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3T5L
  • Community annotation for 3T5L at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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