Research workbench
HIV-1 protease complexed with an inhibitor lp-130
Analyse HIV-1 protease complexed with an inhibitor lp-130 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ODY
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- EC
- 3.4.23.16
- Ligands
- LP1
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 4% helix, 51% strand | — |
Ligands and binding sites
- LP1 · 4-[2-(2-acetylamino-3-naphtalen-1-yl-propionylamino)-4-methyl-pentanoylamino]-3-hydroxy-6-methyl-heptanoic acid [1-(1-carbamoyl-2-naphthalen-1-yl-ethylcarbamoyl)-propyl]-amide · ligand · 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 | 330 | 0.70 | 0.83 | 38 | LP1 |
Interfaces
1 interface between chains.
- A–B · 1866 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 1ODY · HIV-1 protease complexed with an inhibitor lp-130 · 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 1ODY · PDBe 1ODY
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