Research workbench
Crystal structure of HIV-1 protease mutant I54M with antiviral drug amprenavir
Analyse Crystal structure of HIV-1 protease mutant I54M with antiviral drug amprenavir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NU6
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P03366
- Ligands
- 478, NA, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 56% strand | P03366 |
Ligands and binding sites
- 478 · {3-[(4-amino-benzenesulfonyl)-isobutyl-amino]-1-benzyl-2-hydroxy-propyl}-carbamic acid tetrahydro-furan-3-yl ester · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 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 | 315 | 0.72 | 0.85 | 34 | 478 |
Interfaces
1 interface between chains.
- A–B · 1856 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3NU6 · Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir · 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 P03366
- Elsewhere: RCSB PDB 3NU6 · PDBe 3NU6 · UniProt P03366
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