MolNFT v1 · #86687 · protein + DNA
Pfv intasome with inhibitor xz-259
4BE2 · Pfv integrase: “Pfv intasome with inhibitor xz-259”. X-ray diffraction, 4 ligands (XZ2, MG, ZN), 10 pockets (best druggability 0.69). MolNFT v1 #86687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BE2
- 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
- XZ2, MG, ZN, SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase (EC 2.7.7.-) | protein | 368 | 34% helix, 21% strand | P14350 |
| B | Pfv 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) *AP*CP*A)-3' | dna | 17 | — | — |
Ligands and binding sites
- XZ2 · 2-(3-chloro-4-fluorobenzyl)-6,7-dihydroxy-N,N-dimethyl-1-oxo-2,3-dihydro-1H-isoindole-4-sulfonamide · 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, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.78 | 39 | empty |
| 2 | 82 | 0.61 | 0.90 | 25 | empty |
| 3 | 275 | 0.57 | 0.78 | 34 | empty |
| 4 | 52 | 0.54 | 0.89 | 20 | empty |
| 5 | 71 | 0.50 | 0.85 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1446 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 741 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- A–D · 311 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4BE2 · PFV intasome with inhibitor XZ-259 · 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 4BE2 · PDBe 4BE2 · UniProt P14350
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