MolNFT v1 · #102090 · protein
Crystal structure of inactive HIV-1 protease in complex with the P1-P6 substrate variant (L449F)
4OBH: “Crystal structure of inactive HIV-1 protease in complex with the P1-P6 substrate variant (L449F)”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.52). MolNFT v1 #102090 on GenesisL1: 3D structure, binding sites…
- PDB
- 4OBH
- Type
- protein
- Length
- 416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease; P1-P6 peptide
- EC
- 3.4.23.16
- UniProt
- P03369, P03349
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P03369 |
| E, F | P1-P6 peptide | protein | 10 | 0% helix, 30% strand | P03349 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, D, F
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, E, C, F, D
- GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D, F
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.52 | 0.77 | 28 | empty |
| 2 | 154 | 0.42 | 0.74 | 23 | empty |
| 3 | 69 | 0.35 | 0.77 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1845 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1800 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 639 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 619 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 524 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OBH · Crystal Structure of Inactive HIV-1 Protease in Complex with the p1-p6 substrate variant… · 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 P03369
- Every structure of UniProt P03349
- Elsewhere: RCSB PDB 4OBH · PDBe 4OBH · UniProt P03369 · UniProt P03349
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.