3FDS

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

Structural Biology Knowledgebase: 3FDS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3FDS

Classification: TRANSFERASE

Total Structure Weight: 97748.30

Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A 352 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA polymerase sliding clamp B C 249 Sulfolobus solfataricus Mutation: F2V
Gene Name(s): pcn1 pcnA-like SSO0397 C41_008
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA polymerase sliding clamp C D 245 Sulfolobus solfataricus Gene Name(s): pcn2 pcnA-2 SSO1047
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

D TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, C DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, C, D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.99 α = 90.00
b = 86.41 β = 107.30
c = 97.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-11-26
  • Released Date: 2009-01-20
  • Deposition author(s): Ling, H.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4