4FYD

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP

Structural Biology Knowledgebase: 4FYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FYD

Classification: TRANSFERASE / DNA

Total Structure Weight: 230933.75


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase alpha catalytic subunit A A, B 910 Saccharomyces cerevisiae EC#: 2.7.7.7 IUBMB
Fragment: Polymerase domain, UNP residues 349-1258
Mutation: R508A, N509A, D998N
Gene Name(s): POL1 CDC17 YNL102W N2181
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') C, D 25 synthetic
DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') E, F 12 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGT
Query on DGT

A, B 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.210
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 111.69 α = 90.00
b = 145.69 β = 90.00
c = 197.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-04
  • Released Date: 2013-02-27
  • Deposition author(s): Perera, R.L., Pellegrini, L.

Revision History

  • 2014-01-15
    Type: Citation | Details: Citation update
  • 2013-04-24
    Type: Citation | Details: Citation update