Research workbench
Core domain of HIV-1 integrase complexed with mg++ and 1-(5- chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone
Analyse Core domain of HIV-1 integrase complexed with mg++ and 1-(5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QS4
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (HIV-1 integrase (E.C.2.7.7.49))
- EC
- 2.7.7.49
- UniProt
- Q76353
- Ligands
- 100, MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (HIV-1 integrase (E.C.2.7.7.49)) (EC 2.7.7.49) | protein | 150 | 47% helix, 20% strand | Q76353 |
| B | Protein (HIV-1 integrase (E.C.2.7.7.49)) (EC 2.7.7.49) | protein | 152 | 48% helix, 21% strand | Q76353 |
| C | Protein (HIV-1 integrase (E.C.2.7.7.49)) (EC 2.7.7.49) | protein | 151 | 51% helix, 21% strand | Q76353 |
Ligands and binding sites
- 100 · 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.98 | 27 | empty |
| 2 | 241 | 0.55 | 0.77 | 32 | empty |
| 3 | 341 | 0.54 | 0.74 | 32 | empty |
| 4 | 289 | 0.54 | 0.76 | 35 | empty |
| 5 | 101 | 0.46 | 0.80 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1517 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1QS4 · Core domain of HIV-1 integrase complexed with Mg++ and… · 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 Q76353
- Elsewhere: RCSB PDB 1QS4 · PDBe 1QS4 · UniProt Q76353
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.