5WNY

DNA polymerase beta substrate complex with incoming 5-FdUTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 5WNY

Classification: DNA LIGASE / DNA TRANSFERASE

Total Structure Weight: 48445.95


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') T 16 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') P 10 Synthetic construct
DNA (5'-D(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B7P
Query on B7P

A 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate)
5-FdUTP (Synonym)
C9 H14 F N2 O14 P3
YQOCUTDPKPPQGA-RRKCRQDMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.181
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.48 α = 90.00
b = 79.75 β = 107.23
c = 55.57 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-08-01
  • Released Date: 2017-09-13
  • Deposition author(s): Schaich, M.A., Smith, M.R., Cloud, A.S., Holloran, S.M., Freudenthal, B.D.

Revision History

  • Version 1_0: 2017-09-13

    Type: Initial release