5YV3 Dna Binding Protein Dna date Nov 23, 2017
title Dna Polymerase Iv - Dna Ternary Complex 7
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
Expression_system_taxid: 562

Molecule: Dtn1
Chain: G, B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333

Molecule: Dtn2
Chain: H, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
symmetry Space Group: P 1 21 1
R_factor 0.203 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
86.249 57.038 109.950 90.00 94.55 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand DPO, 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 (5yv3.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (5yv3.pdb2.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 5YV3
  • CSU: Contacts of Structural Units for 5YV3
  • Structure Factors (2842 Kb)
  • Retrieve 5YV3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YV3 from S2C, [Save to disk]
  • View 5YV3 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 5YV3
  • 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 5yv3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yv3_H] [5yv3_C] [5yv3_F] [5yv3_G] [5yv3_B] [5yv3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YV3
  • Community annotation for 5YV3 at PDBWiki (http://pdbwiki.org)

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