Research workbench
X-ray structure of ester chemical analogue 'covalent dimer' [ILE50,O- ILE50']HIV-1 protease complexed with mvt-101 inhibitor
Analyse X-ray structure of ester chemical analogue 'covalent dimer' [ILE50,O… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NXE
- 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, 2NC, SO4
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease covalent dimer (EC 3.4.23.16) | protein | 202 | 6% helix, 51% strand | — |
Ligands and binding sites
- OIL · (2S,3S)-2-hydroxy-3-methylpentanoic acid · ligand · chains A
- 2NC · N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide · 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 | 432 | 0.74 | 0.83 | 44 | OIL, 2NC |
Modifications
Observed in the structure: 11 modified, 2 covalent (nonstandard, alkylation, covalent ligand).
Compared structures
- 3NXE · 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 3NXE · PDBe 3NXE
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