MolNFT v1 · #102089 · protein
Crystal structure of nelfinavir-resistant, inactive HIV-1 protease (D30N/N88D) in complex with the P1-P6 substrate.
4OBG: “Crystal structure of nelfinavir-resistant, inactive HIV-1 protease (D30N/N88D) in complex with the P1-P6…”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.48). MolNFT v1 #102089 on GenesisL1: 3D structure, binding…
- PDB
- 4OBG
- Type
- protein
- Length
- 415 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 0.48
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 | 9 | 0% helix, 44% strand | P03349 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.48 | 0.78 | 28 | empty |
| 2 | 70 | 0.46 | 0.83 | 20 | empty |
| 3 | 142 | 0.39 | 0.73 | 35 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1774 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 622 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 569 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 536 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OBG · Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex… · 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 4OBG · PDBe 4OBG · UniProt P03369 · UniProt P03349
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