1BPY

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 1BPY

Classification: TRANSFERASE / DNA

Total Structure Weight: 48237.62


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (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*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T 16 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*DOC)-3') P 10 Synthetic construct
DNA (5'-D(*GP*TP*CP*GP*G)-3') D 5 Synthetic construct

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

A 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A 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
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.232
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.54 α = 90.00
b = 79.82 β = 107.11
c = 54.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-04-15
  • Released Date: 1997-06-16
  • Deposition author(s): Sawaya, M.R., Pelletier, H., Prasad, R., Wilson, S.H., Kraut, J.

Revision History

  • Version 1_0: 1997-06-16

    Type: Initial release

  • Version 1_1: 2008-05-22

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-02-15

    Type: Source and taxonomy, Structure summary