MolNFT v2 · #74533 · protein + DNA
Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI MK0536
3OYH · PFV integrase: “Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI MK0536”. X-ray diffraction at 2.74, 5 ligands (ZYN, MG, ZN), 10 pockets (best druggability 0.69). MolNFT v2 #74533…
- PDB
- 3OYH
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.74
- Source
- Human spumaretrovirus; SYNTHETIC CONSTRUCT
- Molecule
- PFV integrase; DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')…
- UniProt
- P14350
- Ligands
- ZYN, MG, ZN, SO4, NH4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.74 · 4 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PFV integrase | protein | 368 | 35% helix, 21% strand | P14350 |
| B | PFV integrase | protein | 184 | 36% helix, 16% strand | P14350 |
| C | DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') | dna | 19 | — | — |
| D | DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- ZYN · 6-(3-chloro-4-fluorobenzyl)-4-hydroxy-N,N-dimethyl-2-(1-methylethyl)-3,5-dioxo-2,3,5,6,7,8-hexahydro-2,6-naphthyridine-1-carboxamide · ligand · chains A, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, D, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.69 | 0.78 | 40 | empty |
| 2 | 346 | 0.67 | 0.81 | 46 | empty |
| 3 | 70 | 0.49 | 0.84 | 15 | empty |
| 4 | 217 | 0.47 | 0.74 | 25 | MG, ZYN |
| 5 | 78 | 0.45 | 0.81 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1437 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1148 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 734 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–D · 269 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3OYH · Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14350
- Elsewhere: RCSB PDB 3OYH · PDBe 3OYH · UniProt P14350
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