5YUT Dna Binding Protein Dna date Nov 23, 2017
title Dna Polymerase Iv - Dna Ternary Complex 3
authors J.Kottur, D.T.Nair
compound source
Molecule: Dna Polymerase Iv
Chain: F, A
Synonym: Pol Iv,Translesion Synthesis Polymerase Iv,Tsl Pol Iv;
Engineered: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12
Gene: Dinb, Dinp, B0231, Jw0221
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
Expression_system_strain: K-12

Molecule: Dtn
Chain: G, H, B, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
86.750 56.930 110.210 90.00 95.12 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand MG, TTP enzyme Transferase E.C. BRENDA
F, A

Primary referencePyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction., Kottur J, Nair DT, Nucleic Acids Res. 2018 Jul 6;46(12):5875-5885. doi: 10.1093/nar/gky402. PMID:29850882
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (298 Kb) [Save to disk]
  • Biological Unit Coordinates (5yut.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (5yut.pdb2.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 5YUT
  • CSU: Contacts of Structural Units for 5YUT
  • Structure Factors (2804 Kb)
  • Retrieve 5YUT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YUT from S2C, [Save to disk]
  • View 5YUT 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 5YUT
  • 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
  • Fold representative 5yut from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yut_C] [5yut_F] [5yut_B] [5yut_H] [5yut_A] [5yut_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YUT
  • Community annotation for 5YUT at PDBWiki (http://pdbwiki.org)

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