5VI0

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an abasic site analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 5VI0

Classification: HYDROLASE / DNA

Total Structure Weight: 97303.23


Macromolecule Entities
Molecule Chains Length Organism Details
alkylpurine DNA glycosylase AlkC A, B 369 Pseudomonas fluorescens Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3') C, F 11 Synthetic construct
DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') D, E 11 Synthetic construct

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
P4K
Query on P4K

A polyethylene glycol
3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan- 1-ol (Synonym)
C30 H62 O15
WWPGFZAAWXFBTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET
3DR
Query on 3DR
C, F DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.168
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 80.64 α = 90.00
b = 94.93 β = 90.00
c = 134.03 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-04-13
  • Released Date: 2017-10-25
  • Deposition author(s): Shi, R., Eichman, B.F.

Revision History

  • Version 1_0: 2017-10-25

    Type: Initial release

  • Version 1_1: 2017-11-01

    Type: Database references