Research workbench
HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 4
Analyse HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B6L
- 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
- PI4, SO4
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retropepsin (EC 3.4.23.16) | protein | 99 | 4% helix, 55% strand | P03369 |
Ligands and binding sites
- PI4 · 1-[2-(8-carbamoylmethyl-6,9-dioxo-2-oxa-7,10-diaza-bicyclo[11.2.2]heptadeca- 1(16),13(17),14-trien-11-yl)-2-hydroxy-ethyl]-piperidine-2-carboxylic acid tert-butylamide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 335 | 0.71 | 0.83 | 34 | PI4 |
Interfaces
1 interface between chains.
- A–B · 1858 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1B6L · HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 4 · 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 P03369
- Elsewhere: RCSB PDB 1B6L · PDBe 1B6L · UniProt P03369
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