5OMV

Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 5OMV

Classification: TRANSFERASE

Total Structure Weight: 99361.30


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 775 Thermococcus sp. 9on-7 EC#: 2.7.7.7 IUBMB
Mutation: D141A, E143A
Gene Name(s): pol polA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA template T 16 Synthetic construct
DNA primer P 12 Synthetic construct

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

A 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

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

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

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, T 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: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.189
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 66.69 α = 90.00
b = 94.96 β = 90.00
c = 158.74 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-08-01
  • Released Date: 2017-12-20
  • Deposition author(s): Betz, K., Marx, A., Diederichs, K.

Revision History

  • Version 1_0: 2017-12-20

    Type: Initial release