4E3S

RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT

Structural Biology Knowledgebase: 4E3S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E3S

Classification: Transferase / DNA

Total Structure Weight: 114345.66


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L561A, S565G, Y567A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
DNA template T 17 synthetic
DNA primer P 13 synthetic

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

A 3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]- beta-D-erythro-pentofuranosyl}-7-methyl-3H- imidazo[4,5-b]pyridine
C12 H18 N3 O12 P3
LSFMZRZQGVHWHK-IVZWLZJFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.180
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.17 α = 90.00
b = 118.51 β = 90.00
c = 130.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-10
  • Released Date: 2012-05-23
  • Deposition author(s): Xia, S., Wang, J., Konigsberg, W.H.

Revision History

  • 2012-08-15
    Type: Citation | Details: Citation update