Research workbench
Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 5-bromo-1-methyl-1H-indole-2- carboxylic acid (AT21457) in an alternate binding site.
Analyse Structure of hepatitis C virus (HCV) full-length NS3 complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FPY
- Type
- protein
- Length
- 1,287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease NS3
- EC
- 3.4.21.-
- UniProt
- P26663
- Ligands
- R2N
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease NS3 (EC 3.4.21.-) | protein | 645 | 28% helix, 29% strand | P26663 |
| B | Serine protease NS3 (EC 3.4.21.-) | protein | 642 | 27% helix, 29% strand | P26663 |
Ligands and binding sites
- R2N · 5-bromo-1-methyl-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.80 | 0.81 | 126 | empty |
| 2 | 597 | 0.77 | 0.83 | 66 | empty |
| 3 | 237 | 0.67 | 0.84 | 36 | empty |
| 4 | 417 | 0.65 | 0.78 | 42 | empty |
| 5 | 545 | 0.65 | 0.76 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1415 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5FPY · Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand… · 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 P26663
- Elsewhere: RCSB PDB 5FPY · PDBe 5FPY · UniProt P26663
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