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Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal inhibitor (compound 31)
Analyse Crystal structure of the prototype foamy virus intasome with a 2- pyridinone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UOQ
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Nucleotide preprocessed pfv donor DNA (non-transferred strand); Nucleotide…
- EC
- 2.7.7.-
- UniProt
- P14350
- Ligands
- 8G1, MG, ZN, SO4
- Pockets
- 12 · best druggability 0.70
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.-) | protein | 368 | 33% helix, 21% strand | P14350 |
| B | Integrase (EC 2.7.7.-) | protein | 184 | 39% helix, 16% strand | P14350 |
| C | Nucleotide preprocessed pfv donor DNA (non-transferred strand) | dna | 19 | — | — |
| D | Nucleotide preprocessed pfv donor DNA (transferred strand) | dna | 17 | — | — |
Ligands and binding sites
- 8G1 · (3R)-8-[(3-chloro-4-fluorophenyl)methyl]-6-hydroxy-1,5, 7-trioxo-1,2',3',5,7,8,9,10-octahydro-2H-spiro[imidazo[5,1-a][2,6]naphthyridine-3,1'-indene]-7'-carbonitrile · 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 · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.70 | 0.79 | 46 | empty |
| 2 | 342 | 0.68 | 0.82 | 43 | GOL |
| 3 | 54 | 0.52 | 0.88 | 22 | empty |
| 4 | 80 | 0.51 | 0.84 | 15 | empty |
| 5 | 180 | 0.45 | 0.75 | 24 | MG, GOL, 8G1 |
Interfaces
4 interfaces between chains.
- A–B · 1441 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1166 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 738 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–D · 271 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5UOQ · Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal… · 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 5UOQ · PDBe 5UOQ · UniProt P14350
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