Research workbench
HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 5
Analyse HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B6K
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retropepsin
- EC
- 3.4.23.16
- UniProt
- P03369
- Ligands
- PI5, SO4
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retropepsin (EC 3.4.23.16) | protein | 99 | 4% helix, 57% strand | P03369 |
Ligands and binding sites
- PI5 · N-[3-(8-sec-butyl-7,10-dioxo-2-oxa-6,9-diaza-bicyclo[11.2.2]heptadeca-1(16),13(17),14- trien-11-ylamino)-2-hydroxy-1-(4-hydroxy-benzyl)-propyl]-3-methyl-2- (2-oxo-pyrrolidin-1-yl)-butyramide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 420 | 0.72 | 0.82 | 35 | PI5 |
Interfaces
1 interface between chains.
- A–B · 1860 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1B6K · HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 5 · 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 P03369
- Elsewhere: RCSB PDB 1B6K · PDBe 1B6K · UniProt P03369
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