MolNFT v1 · #21908 · protein
Crystal structure of HIV-1 protease complexed with a product of autoproteolysis
1SP5: “Crystal structure of HIV-1 protease complexed with a product of autoproteolysis”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.65). MolNFT v1 #21908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SP5
- Type
- protein
- Length
- 203 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; 5-mer peptide from protease
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- CL
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 55% strand | P03367 |
| I | 5-mer peptide from protease | protein | 5 | 0% helix, 60% strand | P03367 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
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 | 155 | 0.65 | 0.86 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1848 Ų buried · 38 hydrogen bonds · protein-protein
- A–I · 423 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 285 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 1SP5 · Crystal structure of HIV-1 protease complexed with a product of autoproteolysis · 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 1SP5 · PDBe 1SP5 · UniProt P03367
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