Research workbench
The crystal structure of NS5A domain 1 from genotype 1A reveals new clues to the mechanism of action for dimeric HCV inhibitors
Analyse The crystal structure of NS5A domain 1 from genotype 1A reveals new clues to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CL1
- Type
- protein
- Length
- 629 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 5A
- UniProt
- K4KA16
- Ligands
- ZN, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 5A | protein | 155 | 7% helix, 37% strand | K4KA16 |
| B | Non-structural protein 5A | protein | 157 | 5% helix, 38% strand | K4KA16 |
| C | Non-structural protein 5A | protein | 157 | 4% helix, 37% strand | K4KA16 |
| D | Non-structural protein 5A | protein | 160 | 4% helix, 35% strand | K4KA16 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.82 | 0.84 | 77 | empty |
| 2 | 361 | 0.55 | 0.74 | 49 | SO4 |
| 3 | 81 | 0.34 | 0.75 | 21 | empty |
| 4 | 68 | 0.33 | 0.76 | 20 | empty |
| 5 | 61 | 0.31 | 0.75 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–B · 451 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 310 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 306 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4CL1 · The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the… · 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 K4KA16
- Elsewhere: RCSB PDB 4CL1 · PDBe 4CL1 · UniProt K4KA16
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