Research workbench
Crystal structure of nelfinavir-resistant, inactive HIV-1 protease (D30N/N88D) in complex with the P1-P6 substrate variant (L449F/S451N)
Analyse Crystal structure of nelfinavir-resistant, inactive HIV-1 protease (D30N/N88D)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OBD
- 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
- 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 | 9 | 0% helix, 33% strand | P03349 |
| F | P1-P6 peptide | protein | 8 | 0% helix, 38% strand | P03349 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, D, C, A, E
- GOL · Glycerol · additive · chains A, B
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 | 58 | 0.48 | 0.86 | 20 | empty |
| 2 | 147 | 0.42 | 0.75 | 22 | empty |
| 3 | 95 | 0.35 | 0.74 | 25 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1818 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1742 Ų buried · 36 hydrogen bonds · protein-protein
- B–E · 611 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 512 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 492 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4OBD · 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 4OBD · PDBe 4OBD · UniProt P03369 · UniProt P03349
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