Research workbench
Crystal Structure of a Darunavir Resistant HIV-1 Protease
Analyse Crystal Structure of a Darunavir Resistant HIV-1 Protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B18
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Human immunodeficiency virus 1
- Molecule
- Protease
- Ligands
- CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease | protein | 99 | 7% helix, 51% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.72 | 0.80 | 55 | empty |
| 2 | 525 | 0.69 | 0.79 | 43 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1602 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1540 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5B18 · Crystal structure of a darunavir resistant HIV-1 protease · 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 5B18 · PDBe 5B18
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