MolNFT v1 · #73290 · protein
X-ray structure of ester chemical analogue 'covalent dimer' [ILE50,O- ILE50']HIV-1 protease complexed with kvs-1 inhibitor
3NXN · Protease covalent dimer: “X-ray structure of ester chemical analogue 'covalent dimer' [ILE50,O- ILE50']HIV-1 protease complexed with…”. X-ray diffraction, 3 ligands (OIL, KVS, SO4), 1 pocket (best druggability 0.73). MolNFT v1…
- PDB
- 3NXN
- Type
- protein
- Length
- 202 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease covalent dimer
- EC
- 3.4.23.16
- Ligands
- OIL, KVS, SO4
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease covalent dimer (EC 3.4.23.16) | protein | 202 | 4% helix, 53% strand | — |
Ligands and binding sites
- OIL · (2S,3S)-2-hydroxy-3-methylpentanoic acid · ligand · chains A
- KVS · N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl) amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
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 | 455 | 0.73 | 0.83 | 40 | OIL, KVS |
Modifications
Observed in the structure: 11 modified, 2 covalent (nonstandard, alkylation, covalent ligand).
Compared structures
- 3NXN · X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1… · 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
- Elsewhere: RCSB PDB 3NXN · PDBe 3NXN
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