4KLM

DNA polymerase beta matched product complex with Mg2+, 11 h

Structural Biology Knowledgebase: 4KLM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KLM

Classification: TRANSFERASE LYASE / DNA

Total Structure Weight: 48339.67


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
5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' T 16 synthetic
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3' P 11 synthetic
5'-D(P*GP*TP*CP*GP*G)-3' D 5 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PPV
Query on PPV

A PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.188
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.59 α = 90.00
b = 79.76 β = 107.70
c = 55.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-07
  • Released Date: 2013-07-17
  • Deposition author(s): Freudenthal, B.D., Beard, W.A., Shock, D.D., Wilson, S.H.

Revision History

No revisions since initial release