3OYM

Crystal structure of the PFV N224H mutant intasome bound to manganese

Structural Biology Knowledgebase: 3OYM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3OYM

Classification: RECOMBINATION VIRAL PROTEIN / DNA

Total Structure Weight: 101107.85


Macromolecule Entities
Molecule Chains Length Organism Details
PFV integrase A, B 395 Simian foamy virus Fragment: UNP residues 752 to 1143
Mutation: G217S, S218G, N224H
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
HEZ
Query on HEZ

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

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

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

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

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH4
Query on NH4

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.05 α = 90.00
b = 158.05 β = 90.00
c = 122.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-23
  • Released Date: 2010-11-17
  • Deposition author(s): Hare, S., Cherepanov, P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4