Research workbench
HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate nlltqi
Analyse HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate nlltqi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B7V
- Type
- protein
- Length
- 202 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; Peptide
- EC
- 3.4.23.16
- UniProt
- P04587
- Ligands
- LNT, NA, CL
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P04587 |
| C | Peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- LNT · N-[(2S)-2-amino-1,1-dihydroxy-4-methylpentyl]-L-threonine · ligand · chains A, B, C
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · 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 | 108 | 0.66 | 0.90 | 35 | LNT |
Interfaces
3 interfaces between chains.
- A–B · 1877 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3B7V · HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate NLLTQI · 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 P04587
- Elsewhere: RCSB PDB 3B7V · PDBe 3B7V · UniProt P04587
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