MolNFT v1 · #102088 · protein
Crystal structure of nelfinavir-resistant, inactive HIV-1 protease variant (D30N/N88D) in complex with the P1-P6 substrate variant (S451N)
4OBF: “Crystal structure of nelfinavir-resistant, inactive HIV-1 protease variant (D30N/N88D) in complex with the…”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.51). MolNFT v1 #102088 on GenesisL1: 3D structure…
- PDB
- 4OBF
- Type
- protein
- Length
- 413 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 0.51
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 6% helix, 56% strand | P03369 |
| E | P1-P6 peptide | protein | 10 | 0% helix, 30% strand | P03349 |
| F | P1-P6 peptide | protein | 7 | 0% helix, 43% strand | P03349 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, E, C, D, F
- GOL · Glycerol · additive · 4 copies · chains A, B, E, C, D
- ACT · Acetate ion · additive · chains A
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 | 78 | 0.51 | 0.85 | 22 | empty |
| 2 | 156 | 0.43 | 0.74 | 25 | empty |
| 3 | 163 | 0.43 | 0.74 | 28 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1792 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1784 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 628 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 543 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 502 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4OBF · Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease Variant (D30N/N88D) in… · 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 4OBF · PDBe 4OBF · UniProt P03369 · UniProt P03349
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