1L5U

Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 12 base pairs of duplex DNA following addition of a dTTP, a dATP, and a dCTP residue.

Structural Biology Knowledgebase: 1L5U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 1L5U

Classification: TRANSFERASE / DNA

Total Structure Weight: 75741.28


Macromolecule Entities
Molecule Chains Length Organism Details
DNA Polymerase I A 580 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: Bacillus Fragment (analogous to the E. coli Klenow Fragment)
Gene Name(s): polA pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-3' B 12 synthetic primer strand
5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3' C 16 synthetic template strand

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

A SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.195
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 87.47 α = 90.00
b = 93.42 β = 90.00
c = 105.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-08
  • Released Date: 2003-03-25
  • Deposition author(s): Johnson, S.J., Taylor, J.S., Beese, L.S.

Revision History

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