3OYA

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and raltegravir at 2.65 resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 3OYA

Classification: RECOMBINATION VIRAL PROTEIN / DNA

Total Structure Weight: 101104.86


Macromolecule Entities
Molecule Chains Length Organism Details
PFV integrase A, B 395 Simian foamy virus Mutation: G217S, S218G
Gene Name(s): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') C 19 synthetic 19 nucleotide preprocessed PFV donor DNA (non-transferred strand)
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') D 17 synthetic 17 nucleotide preprocessed PFV donor DNA (transferred strand)

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RLT
Query on RLT

A N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1- methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)- 6-oxo-1,6-dihydropyrimidine-4-carboxamide
MK0518, (Synonym)
C20 H21 F N6 O5
CZFFBEXEKNGXKS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH4
Query on NH4

A AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.205
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 159.76 α = 90.00
b = 159.76 β = 90.00
c = 124.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-23
  • Released Date: 2010-10-20
  • Deposition author(s): Hare, S., Cherepanov, P.
  • Previous versions: 3L2T

Revision History

  • 2011-07-13
    Type: Version format compliance