MolNFT v1 · #119290 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ419 (compound 4C)
5FRN · Integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ419…”. X-ray diffraction, 4 ligands (QUW, MG, ZN), 11 pockets (best druggability 0.72). MolNFT v1 #119290 on…
- PDB
- 5FRN
- Type
- protein + DNA
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-
- UniProt
- P14350
- Ligands
- QUW, MG, ZN, SO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 367 | 35% helix, 21% strand | P14350 |
| B | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 183 | 35% 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
- QUW · 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide · ligand · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, B
- GOL · Glycerol · additive · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.72 | 0.82 | 62 | GOL |
| 2 | 498 | 0.67 | 0.78 | 38 | GOL |
| 3 | 78 | 0.52 | 0.85 | 15 | empty |
| 4 | 197 | 0.52 | 0.77 | 30 | SO4 |
| 5 | 94 | 0.46 | 0.81 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1484 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1135 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 734 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- A–D · 296 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5FRN · 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 5FRN · PDBe 5FRN · UniProt P14350
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