5YYD

DNA polymerase IV - ternary complex 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

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
DTN2G,H,B,C18Escherichia coli K-12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
TTW
Query on TTW

Download SDF File 
Download CCD File 
A, F
5'-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine
C10 H18 N3 O13 P3
RTOWUXJWTDSUGC-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.650α = 90.00
b = 57.050β = 94.94
c = 110.330γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-08 
  • Released Date: 2018-09-05 
  • Deposition Author(s): Kottur, J., Nair, D.T.

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release