4ELU

Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines

Structural Biology Knowledgebase: 4ELU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4ELU

Classification: TRANSFERASE / DNA

Total Structure Weight: 71733.04


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, thermostable A 540 Thermus aquaticus EC#: 2.7.7.7 IUBMB
Fragment: UNP RESIDUES 293-832
Gene Name(s): polA pol1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3') B 12 Synthetic construct DNA primer
DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C 16 Synthetic construct DNA template

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0R6
Query on 0R6

A 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'- (tetrahydrogen triphosphate)
C19 H20 N3 O13 P3
CPJFKEBWOPVPDF-GVDBMIGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A, B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, C ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DDG
Query on DDG
B DNA LINKING C10 H14 N5 O6 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.155
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.21 α = 90.00
b = 108.21 β = 90.00
c = 90.40 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-11
  • Released Date: 2013-03-27
  • Deposition author(s): Marx, A., Diederichs, K., Obeid, S.

Revision History

No revisions since initial release