4J2D

RB69 DNA Polymerase L415K Ternary Complex

Structural Biology Knowledgebase: 4J2D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 4J2D

Classification: Transferase / DNA

Total Structure Weight: 114776.85


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 901 Escherichia virus rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L415K
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') T 18 synthetic
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*T)-3') P 13 synthetic

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

A THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.170
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.44 α = 90.00
b = 119.81 β = 90.00
c = 130.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-04
  • Released Date: 2014-02-19
  • Deposition author(s): Xia, S., Wang, J., Konigsberg, W.H.

Revision History

No revisions since initial release