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Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site.
Analyse Crystal structures of HIV protease V82A and L90M mutants reveal changes in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SDV
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease retropepsin
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- MK1, CL
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease retropepsin (EC 3.4.23.16) | protein | 99 | 4% helix, 54% strand | P03367 |
Ligands and binding sites
- MK1 · N-[2(R)-hydroxy-1(S)-indanyl]-5-[(2(S)-tertiary butylaminocarbonyl)-4(3-pyridylmethyl)piperazino]-4(S)-hydroxy-2(R)-phenylmethylpentanamide · ligand · chains A, B
- CL · Chloride ion · ion · 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 | 362 | 0.71 | 0.83 | 41 | MK1 |
Interfaces
1 interface between chains.
- A–B · 1866 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1SDV · Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir… · 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 P03367
- Elsewhere: RCSB PDB 1SDV · PDBe 1SDV · UniProt P03367
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