MolNFT v1 · #21542 · protein
Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site.
1SDU · Protease retropepsin: “Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site.”. X-ray diffraction, 2 ligands (MK1, SO4), 1 pocket (best druggability 0.72). MolNFT v1 #21542 on GenesisL1…
- PDB
- 1SDU
- 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, SO4
- 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 retropepsin (EC 3.4.23.16) | protein | 99 | 7% helix, 56% 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
- SO4 · Sulfate ion · ion · chains A, B
- ACT · Acetate ion · additive · chains 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 | 355 | 0.72 | 0.84 | 34 | MK1 |
Interfaces
1 interface between chains.
- A–B · 1829 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1SDU · 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 1SDU · PDBe 1SDU · UniProt P03367
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