Research workbench
Two hepatitis C virus NS3 helicase domains complexed with the same strand of DNA
Analyse Two hepatitis C virus NS3 helicase domains complexed with the same strand of DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F55
- Type
- protein + DNA
- Length
- 1,312 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU) P*(DU)P*(DU)P*(DU)P*(DU)P*(DU))-3'…
- EC
- 3.6.1.-
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU)P*(DU) P*(DU)P*(DU)P*(DU)P*(DU)P*(DU))-3' | dna | 13 | — | — |
| E | 5'-D(P*(DU)P*(DU)P*(DU))-3' | dna | 3 | — | — |
| A, B, C | Polyprotein (EC 3.6.1.-) | protein | 432 | 31% helix, 19% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.84 | 0.85 | 111 | empty |
| 2 | 1014 | 0.79 | 0.81 | 85 | SO4 |
| 3 | 726 | 0.71 | 0.78 | 57 | empty |
| 4 | 368 | 0.59 | 0.76 | 47 | empty |
| 5 | 268 | 0.52 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- D–A · 1030 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 923 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 796 Ų buried · 3 hydrogen bonds · protein-protein
- D–B · 707 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–C · 429 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2F55 · Two hepatitis c virus ns3 helicase domains complexed with the same strand of dna · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 2F55 · PDBe 2F55
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