MolNFT v1 · #112706 · protein + DNA
Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal inhibitor
4ZTF · Integrase: “Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal inhibitor”. X-ray diffraction, 4 ligands (X2P, MG, ZN), 10 pockets (best druggability 0.70). MolNFT v1 #112706 on GenesisL1: 3D…
- PDB
- 4ZTF
- 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…
- UniProt
- P14350
- Ligands
- X2P, MG, ZN, SO4
- Pockets
- 10 · 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 | protein | 368 | 33% helix, 21% strand | P14350 |
| B | Integrase | protein | 184 | 39% helix, 17% 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
- X2P · (1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione · ligand · chains A, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.70 | 0.79 | 49 | empty |
| 2 | 344 | 0.68 | 0.82 | 46 | GOL |
| 3 | 139 | 0.58 | 0.83 | 29 | empty |
| 4 | 218 | 0.48 | 0.75 | 24 | X2P, MG |
| 5 | 146 | 0.44 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1433 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1162 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 739 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–D · 269 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4ZTF · Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridi Aminal Inhibitor · 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 4ZTF · PDBe 4ZTF · UniProt P14350
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