5NKL

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 5NKL

Classification: TRANSFERASE

Total Structure Weight: 70993.00


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, thermostable A 540 Thermus aquaticus EC#: 2.7.7.7 IUBMB
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*(DOC))-3') B 12 Synthetic construct
DNA (5'-D(*AP*AP*AP*(DNU)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C 16 Synthetic construct

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
91R
Query on 91R

A [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent- 1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan- 2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C14 H21 N2 O16 P3
JIVPAQSXWIKFCI-CIQGVGRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
91T
Query on 91T

A [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent- 1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan- 2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C14 H21 N2 O16 P3
JIVPAQSXWIKFCI-GFQSEFKGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
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 2 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
B DNA LINKING C9 H14 N3 O6 P DC
91N
Query on 91N
C NON-POLYMER C15 H16 N3 O6 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 108.78 α = 90.00
b = 108.78 β = 90.00
c = 90.57 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-31
  • Released Date: 2017-06-28
  • Deposition author(s): Betz, K., Marx, A., Diederichs, K., Hirao, I., Kimoto, M.

Revision History

  • 2017-07-05
    Type: Database references