MolNFT v1 · #117310 · protein
The spring alpha-helix coordinates multiple modes of HCV NS3 helicase action
5E4F · Serine protease NS3: “The spring alpha-helix coordinates multiple modes of HCV NS3 helicase action”. X-ray diffraction, 3 ligands (ALF, ADP, MG), 7 pockets (best druggability 0.83). MolNFT v1 #117310 on GenesisL1: 3D structure…
- PDB
- 5E4F
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease NS3
- EC
- 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- Q9WMX2
- Ligands
- ALF, ADP, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 437 | 35% helix, 21% strand | Q9WMX2 |
| B | Serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 429 | 34% helix, 21% strand | Q9WMX2 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.83 | 0.84 | 115 | empty |
| 2 | 1198 | 0.74 | 0.77 | 84 | empty |
| 3 | 260 | 0.61 | 0.80 | 35 | ALF, ADP, MG |
| 4 | 245 | 0.60 | 0.80 | 35 | ALF, ADP, MG |
| 5 | 146 | 0.43 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5E4F · The spring alpha-helix coordinates multiple modes of HCV NS3 helicase action · the same entry in another collection · chain B against B, 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 Q9WMX2
- Elsewhere: RCSB PDB 5E4F · PDBe 5E4F · UniProt Q9WMX2
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