Research workbench
HIV protease (pr) with tl-3 in active site and 4-methylbenzene-1,2- diamine in exosite
Analyse HIV protease (pr) with tl-3 in active site and 4-methylbenzene-1,2- diamine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VEA
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- EC
- 3.4.23.16
- UniProt
- Q72863
- Ligands
- 3TL, 9AY
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 4% helix, 49% strand | Q72863 |
Ligands and binding sites
- 3TL · benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate · ligand · chains A
- 9AY · 4-methylbenzene-1,2-diamine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.48 | 0.78 | 22 | empty |
| 2 | 66 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 5VEA · HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite · 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 Q72863
- Elsewhere: RCSB PDB 5VEA · PDBe 5VEA · UniProt Q72863
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