MolNFT v1 · #36796 · protein
X-ray crystal structure of HIV-1 protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant THR80 in HIV-1 protease structure, function, and viral infectivity.
2FGU: “X-ray crystal structure of HIV-1 protease T80S variant in complex with the inhibitor saquinavir used to…”. X-ray diffraction, 4 ligands (QNC, DIQ, NTB), 1 pocket (best druggability 0.65). MolNFT v1 #36796 on GenesisL1: 3D structure…
- PDB
- 2FGU
- Type
- protein
- Length
- 200 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- O38716
- Ligands
- QNC, DIQ, NTB, PO4
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease (EC 3.4.23.16) | protein | 101 | 4% helix, 53% strand | O38716 |
| B | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 54% strand | O38716 |
Ligands and binding sites
- QNC · quinoline-2-carboxylic acid · ligand · chains A, B
- DIQ · 2-methyl-decahydro-isoquinoline-3-carboxylic acid · ligand · chains A, B
- NTB · Tertiary-butylamine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.65 | 0.84 | 23 | DIQ, NTB |
Interfaces
1 interface between chains.
- A–B · 1869 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2FGU · X-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor… · the same entry in another collection · chain B against B, 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 O38716
- Elsewhere: RCSB PDB 2FGU · PDBe 2FGU · UniProt O38716
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