4TQS Transferase Dna date Jun 11, 2014
title Ternary Complex Of Y-Family Dna Polymerase Dpo4 With (5'S)-8 2'-Deoxyguanosine And Dctp
authors L.Zhao
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
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(Gpgpgpgpgpapapgpgpaptpt)-3'
Chain: C, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Ptpcpapcp(2lf) Pgpapaptpcpcptptpcpcpcpcpc)-3');
Chain: D, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.228 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.120 184.242 52.124 90.00 110.09 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand 2LF, DCP, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceKinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA Replication Stalling., Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson SM, Zhao L, Biochemistry. 2015 Jan 13. PMID:25569151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (4tqs.pdb1.gz) 130 Kb
  • Biological Unit Coordinates (4tqs.pdb2.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 4TQS
  • CSU: Contacts of Structural Units for 4TQS
  • Structure Factors (1006 Kb)
  • Retrieve 4TQS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4TQS from S2C, [Save to disk]
  • Re-refined 4tqs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4TQS 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 4TQS
  • 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 4TQS, from MSDmotif at EBI
  • Fold representative 4tqs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4tqs_C] [4tqs_B] [4tqs_P] [4tqs_D] [4tqs] [4tqs_A] [4tqs_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4TQS
  • Community annotation for 4TQS at PDBWiki (http://pdbwiki.org)

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