Research workbench
Pfv intasome with inhibitor xz-90
Analyse Pfv intasome with inhibitor xz-90 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BDZ
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfv integrase; 19 nucleotide preprocessed pfv donor DNA (non-transferred strand); 17…
- EC
- 2.7.7.-
- UniProt
- P14350
- Ligands
- 19C, MG, ZN, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase (EC 2.7.7.-) | protein | 368 | 33% helix, 21% strand | P14350 |
| B | Pfv integrase (EC 2.7.7.-) | protein | 184 | 36% 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
- 19C · 2-[(3-chloranyl-4-fluoranyl-phenyl)methyl]-6,7-bis(oxidanyl)isoindol-1-one · 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 | 579 | 0.69 | 0.78 | 48 | empty |
| 2 | 361 | 0.67 | 0.81 | 54 | empty |
| 3 | 61 | 0.59 | 0.91 | 20 | empty |
| 4 | 189 | 0.51 | 0.77 | 25 | SO4 |
| 5 | 67 | 0.49 | 0.84 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1454 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1145 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 736 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–D · 272 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4BDZ · PFV intasome with inhibitor XZ-90 · 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 4BDZ · PDBe 4BDZ · UniProt P14350
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