5GNQ

Crystal structure of replisomal dimer of DNA polymerase from bacteriophage RB69 with DNA duplexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 5GNQ

Classification: TRANSFERASE / DNA

Total Structure Weight: 232214.80


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B 908 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*TP*C)-3') S, T 19 Synthetic construct
DNA (5'-D(*GP*AP*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3') P, Q 15 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DUP
Query on DUP

A 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
5GP
Query on 5GP

A, B GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.181
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 164.60 α = 90.00
b = 164.60 β = 90.00
c = 165.77 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-07-24
  • Released Date: 2017-07-26
  • Deposition author(s): Youn, H.-S., Lee, Y., Kang, J.Y., An, J.Y., Lee, J.-G., Park, K.R., Lim, J.J., Wang, J., Eom, S.H.

Revision History

  • Version 1_0: 2017-07-26

    Type: Initial release

  • Version 1_1: 2017-10-18

    Type: Author supporting evidence