5YV4

DNA polymerase IV - DNA ternary complex 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

Kottur, J.Nair, D.T.

(2018) Nucleic Acids Res. 46: 5875-5885


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
F, A
352Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dinB (dinP)
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47155
Entity ID: 2
MoleculeChainsLengthOrganism
DTN1G,B18Escherichia coli K-12
Entity ID: 3
MoleculeChainsLengthOrganism
DTN2H,C19Escherichia coli K-12
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
DPO
Query on DPO

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Download CCD File 
A, F
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 57.160β = 94.49
c = 110.580γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-23 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Kottur, J., Nair, D.T.

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release