5MMB

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ434 (compound 6p)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 5MMB

Classification: VIRAL PROTEIN

Total Structure Weight: 102378.03


Macromolecule Entities
Molecule Chains Length Organism Details
PFV 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 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OUY
Query on OUY

A methyl 3-[5-azanyl-6-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]- 8-oxidanyl-7-oxidanylidene-1,8-naphthyridin- 3-yl]propanoate
C20 H18 F2 N4 O5
JVWFVALMCGSXOC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEZ
Query on HEZ

A, B 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 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: 2.77 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.184
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 160.49 α = 90.00
b = 160.49 β = 90.00
c = 123.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-12-09
  • Released Date: 2017-08-02
  • Deposition author(s): Maskell, D.P., 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