MolNFT v1 · #119289 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ384 (compound 4A)
5FRM · Pfv integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti XZ384…”. X-ray diffraction, 4 ligands (WA5, MG, ZN), 9 pockets (best druggability 0.68). MolNFT v1 #119289 on…
- PDB
- 5FRM
- Type
- protein + DNA
- Length
- 586 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
- WA5, MG, ZN, SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase | protein | 367 | 35% helix, 21% strand | P14350 |
| B | Pfv integrase | protein | 183 | 37% 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
- WA5 · 4-azanylidene-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-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 · 8 copies · chains A, D, C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.68 | 0.82 | 51 | GOL |
| 2 | 510 | 0.68 | 0.78 | 42 | GOL |
| 3 | 63 | 0.51 | 0.86 | 15 | empty |
| 4 | 179 | 0.50 | 0.77 | 25 | SO4 |
| 5 | 175 | 0.46 | 0.75 | 23 | MG, MES, SO4, WA5 |
Interfaces
4 interfaces between chains.
- A–B · 1485 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1139 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 739 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–D · 303 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5FRM · 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 5FRM · PDBe 5FRM · UniProt P14350
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