5VHV

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.141

Literature

Macromolecules
Sequence Display for 5VHV

Classification: HYDROLASE / DNA

Total Structure Weight: 95892.70


Macromolecule Entities
Molecule Chains Length Organism Details
alkylpurine DNA glycosylase AlkC A, B 361 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*(NRI)P*GP*TP*CP*T)-3') C, E 11 Synthetic construct
DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') D, F 11 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
9B4
Query on 9B4

D, F (2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)- 2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14- tetraoxaheptadecane-2,16-diol
Pentaerythritol propoxylate (5/4 PO/OH) (Synonym)
C20 H42 O9
XAZUABIGWFVOAV-FVVUREQNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A, B 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

C, E SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
NRI
Query on NRI
C, E DNA LINKING C5 H12 N O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.141
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 198.37 α = 90.00
b = 198.37 β = 90.00
c = 60.19 γ = 120.00

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