1JX4

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Structural Biology Knowledgebase: 1JX4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 1JX4

Classification: TRANSFERASE / DNA

Total Structure Weight: 50458.50


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV (family Y) A 352 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Mutation: M1M, M76M, M89M, M157M, M216M, M251M
Gene Name(s): dbh dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' P 13 synthetic
5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' T 18 synthetic

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

A 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O8 P2
QYFSANXOEHYVFG-NKWVEPMBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.213
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.09 α = 90.00
b = 102.82 β = 90.00
c = 52.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-05
  • Released Date: 2001-10-05
  • Deposition author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4