Research workbench
Crystal structure of multidrug resistant HIV-1 protease clinical isolate PR20D25N with tucked flap
Analyse Crystal structure of multidrug resistant HIV-1 protease clinical isolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z50
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- UniProt
- Q0PQ60
- Ligands
- NA, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease | protein | 99 | 6% helix, 55% strand | Q0PQ60 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.76 | 0.80 | 58 | empty |
| 2 | 379 | 0.54 | 0.73 | 37 | empty |
| 3 | 74 | 0.32 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1577 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1442 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 200 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 102 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4Z50 · Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20D25N with… · 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 Q0PQ60
- Elsewhere: RCSB PDB 4Z50 · PDBe 4Z50 · UniProt Q0PQ60
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