4JV1

Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming dgtp

Structural Biology Knowledgebase: 4JV1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 4JV1

Classification: TRANSFERASE / DNA

Total Structure Weight: 49235.16


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A 347 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*(HN1)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') B 15 synthetic
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') C 13 synthetic

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

A 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
HN1
Query on HN1
B DNA LINKING C19 H30 N5 O9 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.213
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.27 α = 90.00
b = 102.18 β = 90.00
c = 52.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-25
  • Released Date: 2013-08-28
  • Deposition author(s): Banerjee, S., Shanmugam, G., Stone, M.P.

Revision History

  • 2013-10-09
    Type: Citation | Details: Citation update