MolNFT v1 · #119291 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ446 (compound 4F)
5FRO · Pfv integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ446…”. X-ray diffraction, 4 ligands (XXJ, MG, ZN), 11 pockets (best druggability 0.70). MolNFT v1 #119291 on…
- PDB
- 5FRO
- Type
- protein + DNA
- Length
- 585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfv integrase; 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
- XXJ, MG, ZN, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase | protein | 367 | 34% helix, 21% strand | P14350 |
| B | Pfv integrase | protein | 182 | 38% helix, 16% strand | P14350 |
| C | 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 | 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
- XXJ · 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-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 · 5 copies · chains A, D, B
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.70 | 0.79 | 41 | GOL |
| 2 | 360 | 0.67 | 0.81 | 55 | GOL |
| 3 | 55 | 0.57 | 0.90 | 20 | empty |
| 4 | 182 | 0.51 | 0.77 | 27 | SO4 |
| 5 | 74 | 0.51 | 0.84 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1472 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1147 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 740 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–D · 306 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5FRO · 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 5FRO · PDBe 5FRO · UniProt P14350
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