5VU8

TNA polymerase, closed ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.258

Literature

Macromolecules
Sequence Display for 5VU8

Classification: TRANSFERASE / DNA

Total Structure Weight: 99221.26


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 774 Thermococcus kodakarensis EC#: 2.7.7.7 IUBMB
Mutation: D141A, E143A, E147H, A485R, E584K, E664I
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA template T 16 Synthetic construct
DNA/TNA hybrid primer P 12 Synthetic construct

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
9O7
Query on 9O7

A [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)- 4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate
C9 H14 N5 O12 P3
AWDFERYZHFHVNT-AFEQZKEHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, P 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
9O4
Query on 9O4
P DNA linking C9 H12 N5 O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.258
  • Space Group: P 2 21 21

Unit Cell:

Length (Å) Angle (°)
a = 72.29 α = 90.00
b = 107.36 β = 90.00
c = 147.73 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-05-18
  • Released Date: 2017-12-06
  • Deposition author(s): Chim, N., Chaput, J.C.

Revision History

  • Version 1_0: 2017-12-06

    Type: Initial release