5NO1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ407 (compound 5g)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 5NO1

Classification: VIRAL PROTEIN

Total Structure Weight: 102164.77


Macromolecule Entities
Molecule Chains Length Organism Details
Integrase A, B 395 Simian foamy virus EC#: 2.7.7 IUBMB 2.7.7.49 IUBMB 2.7.7.7 IUBMB 3.1 IUBMB 3.1.26.4 IUBMB 3.4.23 IUBMB
Mutation: G217S, S218G
Details: G217S, S218G = natural variance
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 construct
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') D 17 Synthetic construct

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XZ4
Query on XZ4

A methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]- 7-methoxy-1-oxidanyl-2-oxidanylidene-1,8- naphthyridin-4-yl]amino]ethanoate
C20 H18 F2 N4 O6
NXNKYHOHXLLTIR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

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

A HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B, C 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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.176
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 158.57 α = 90.00
b = 158.57 β = 90.00
c = 123.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-10
  • Released Date: 2017-08-02
  • Deposition author(s): Pye, V.E., Cherepanov, P.

Revision History

  • Version 1_0: 2017-08-02

    Type: Initial release

  • Version 1_1: 2017-09-27

    Type: Database references