Research workbench
Avoiding drug resistance against HCV NS3/4A protease inhibitors
Analyse Avoiding drug resistance against HCV NS3/4A protease inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5M
- Type
- protein
- Length
- 401 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3/4A; Fdemeec peptide
- EC
- 3.4.21.98
- UniProt
- A8DG50, Q9WPH5
- Ligands
- ACE, ZN, SO4
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NS3/4A (EC 3.4.21.98) | protein | 197 | 13% helix, 43% strand | A8DG50 |
| C | Fdemeec peptide | protein | 7 | 0% helix, 57% strand | Q9WPH5 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
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 | 63 | 0.38 | 0.79 | 17 | empty |
| 2 | 133 | 0.38 | 0.74 | 22 | empty |
| 3 | 91 | 0.35 | 0.75 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–C · 551 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3M5M · Avoiding drug resistance against HCV NS3/4A protease inhibitors · the same entry in another collection · chain C against C, 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 A8DG50
- Every structure of UniProt Q9WPH5
- Elsewhere: RCSB PDB 3M5M · PDBe 3M5M · UniProt A8DG50 · UniProt Q9WPH5
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