3LDS

Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG

Structural Biology Knowledgebase: 3LDS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3LDS

Classification: transferase / DNA

Total Structure Weight: 115284.44


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
Details: gp43
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))-3') P 14 synthetic primer
DNA (5'-D(*CP*AP*(8OG)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') T 18 synthetic template

Small Molecules
Ligands 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

P, T SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DDG
Query on DDG
P DNA LINKING C10 H14 N5 O6 P DG
8OG
Query on 8OG
T DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.242
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.01 α = 90.00
b = 121.00 β = 90.00
c = 128.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-01-13
  • Released Date: 2010-06-02
  • Deposition author(s): Hogg, M., Midkiff, J., Rudnicki, J., Reha-Krantz, L, Doublie, S., Wallace, S.S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4