4LVS

DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min

Structural Biology Knowledgebase: 4LVS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4LVS

Classification: Transferase lyase / DNA

Total Structure Weight: 48575.12


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

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)
MN
Query on MN

A, P, T MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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: 2.0 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.216
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 54.98 α = 90.00
b = 78.51 β = 113.24
c = 55.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-26
  • Released Date: 2013-09-04
  • Deposition author(s): Freudenthal, B.D., Beard, W.A., Shock, D.D., Wilson, S.H.
  • Previous versions: 4KLP

Revision History

No revisions since initial release