MolNFT v1 · #121221 · protein
Structural basis for inhibitor-induced aggregation of HIV-1 integrase
5HOT: “Structural basis for inhibitor-induced aggregation of HIV-1 integrase”. X-ray diffraction, 1 ligand (2SQ), 6 pockets (best druggability 0.67). MolNFT v1 #121221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HOT
- Type
- protein
- Length
- 422 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- Q72498
- Ligands
- 2SQ
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 209 | 35% helix, 22% strand | Q72498 |
| B | Integrase (EC 2.7.7.-) | protein | 213 | 39% helix, 20% strand | Q72498 |
Ligands and binding sites
- 2SQ · (2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.67 | 0.96 | 17 | empty |
| 2 | 124 | 0.53 | 0.81 | 28 | empty |
| 3 | 140 | 0.51 | 0.80 | 25 | empty |
| 4 | 128 | 0.51 | 0.80 | 22 | 2SQ |
| 5 | 182 | 0.50 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1643 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5HOT · Structural Basis for Inhibitor-Induced Aggregation of HIV-1 Integrase · 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 Q72498
- Elsewhere: RCSB PDB 5HOT · PDBe 5HOT · UniProt Q72498
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