MolNFT v1 · #69447 · protein + DNA
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism
3KQU · Serine PROTEASE/NTPASE/HELICASE NS3: “Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism”. X-ray diffraction, 3 ligands (BEF, ADP, MN), 20 pockets (best druggability 0.84).…
- PDB
- 3KQU
- Type
- protein + DNA
- Length
- 2,658 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine PROTEASE/NTPASE/HELICASE NS3; 5'-D(*T*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*…
- EC
- 3.4.21.98, 3.6.1.15, 3.6.1.-
- UniProt
- Q9WMX2
- Ligands
- BEF, ADP, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Serine PROTEASE/NTPASE/HELICASE NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.1.-) | protein | 437 | 34% helix, 21% strand | Q9WMX2 |
| M, N | 5'-D(*T*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP* T)-3' | dna | 18 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 6 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.84 | 0.85 | 144 | empty |
| 2 | 935 | 0.83 | 0.84 | 136 | empty |
| 3 | 908 | 0.80 | 0.82 | 86 | empty |
| 4 | 914 | 0.80 | 0.82 | 84 | empty |
| 5 | 310 | 0.78 | 0.90 | 39 | empty |
Interfaces
14 interfaces between chains.
- E–N · 1152 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–N · 1149 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–M · 1147 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–M · 1145 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 762 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3KQU · Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet… · 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 Q9WMX2
- Elsewhere: RCSB PDB 3KQU · PDBe 3KQU · UniProt Q9WMX2
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