Research workbench
Crystal structure analysis of HIV-1 subtype C protease complexed with nelfinavir
Analyse Crystal structure analysis of HIV-1 subtype C protease complexed with nelfinavir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R5Q
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- UniProt
- Q50CM2
- Ligands
- 1UN
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease | protein | 99 | 4% helix, 55% strand | Q50CM2 |
Ligands and binding sites
- 1UN · 2-[2-hydroxy-3-(3-hydroxy-2-methyl-benzoylamino)-4-phenyl sulfanyl-butyl]-decahydro-isoquinoline-3-carboxylic acid tert-butylamide · ligand · 2 copies · chains A, B, C, 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 | 385 | 0.75 | 0.85 | 36 | 1UN |
| 2 | 386 | 0.74 | 0.85 | 36 | 1UN |
| 3 | 158 | 0.44 | 0.75 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1877 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1877 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2R5Q · Crystal Structure Analysis of HIV-1 Subtype C Protease Complexed with Nelfinavir · 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 Q50CM2
- Elsewhere: RCSB PDB 2R5Q · PDBe 2R5Q · UniProt Q50CM2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.