2P66

Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA

Structural Biology Knowledgebase: 2P66 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 2P66

Classification: transferase lyase / DNA

Total Structure Weight: 48325.55


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 335 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Gene Name(s): POLB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') B 16 synthetic
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') C 11 synthetic
DNA (5'-D(P*(3DR)P*GP*TP*CP*GP*G)-3') D 6 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, C SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
D DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.217
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.70 α = 90.00
b = 81.10 β = 108.60
c = 54.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-16
  • Released Date: 2007-04-10
  • Deposition author(s): Prasad, R., Batra, V.K., Yang, X.-P., Krahn, J.M., Pedersen, L.C., Beard, W.A., Wilson, S.H.

Revision History

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