Research workbench
Viability of a drug-resistant HIV-1 protease variant: structural insights for better anti-viral therapy
Analyse Viability of a drug-resistant HIV-1 protease variant: structural insights for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N49
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P03369
- Ligands
- RIT
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 55% strand | P03369 |
Ligands and binding sites
- RIT · Ritonavir · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 0.67 | 0.78 | 60 | RIT |
| 2 | 388 | 0.67 | 0.80 | 40 | RIT |
| 3 | 98 | 0.43 | 0.78 | 20 | empty |
| 4 | 123 | 0.39 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1773 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1737 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 231 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1N49 · Viability of a Drug-Resistant HIV-1 Protease Variant: Structural Insights for Better… · 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 1N49 · PDBe 1N49 · UniProt P03369
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