Research workbench
Pfv intasome with inhibitor xz-89
Analyse Pfv intasome with inhibitor xz-89 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BDY
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; 19 nucleotide preprocessed pfv donor DNA (non-transferred strand); 17…
- EC
- 2.7.7.-
- UniProt
- P14350
- Ligands
- CIJ, MG, ZN, SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 368 | 35% helix, 21% strand | P14350 |
| B | Integrase (EC 2.7.7.-) | protein | 184 | 39% helix, 16% strand | P14350 |
| C | 19 nucleotide preprocessed pfv donor DNA (non-transferred strand) | dna | 19 | — | — |
| D | 17 nucleotide preprocessed pfv donor DNA (transferred strand) | dna | 17 | — | — |
Ligands and binding sites
- CIJ · 2-(3-chloro-4-fluorobenzyl)-4,5-dihydroxy-1H-isoindole-1,3(2H)-dione · ligand · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, C, B
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 | 527 | 0.68 | 0.78 | 38 | empty |
| 2 | 378 | 0.67 | 0.81 | 51 | empty |
| 3 | 50 | 0.55 | 0.90 | 18 | empty |
| 4 | 80 | 0.53 | 0.85 | 15 | empty |
| 5 | 193 | 0.46 | 0.74 | 24 | MG, CIJ, SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1432 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1158 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 735 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–D · 274 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4BDY · PFV intasome with inhibitor XZ-89 · 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 4BDY · PDBe 4BDY · UniProt P14350
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