MolNFT v1 · #74489 · protein + DNA
Crystal structure of the prototype foamy virus (pfv) intasome in complex with manganese at 2.55 resolution
3OY9 · Pfv integrase: “Crystal structure of the prototype foamy virus (pfv) intasome in complex with manganese at 2.55 resolution”. X-ray diffraction, 4 ligands (MN, ZN, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #74489 on…
- PDB
- 3OY9
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- MN, ZN, SO4, NH4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase | protein | 368 | 34% 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
- MN · Manganese (II) 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.69 | 0.78 | 45 | empty |
| 2 | 356 | 0.67 | 0.81 | 44 | empty |
| 3 | 111 | 0.56 | 0.84 | 26 | empty |
| 4 | 188 | 0.51 | 0.77 | 25 | SO4 |
| 5 | 93 | 0.45 | 0.80 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1437 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1152 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–D · 746 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–D · 359 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3OY9 · Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese… · 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 3OY9 · PDBe 3OY9 · UniProt P14350
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