Research workbench
Structure of the catalytic domain of hepatitis C virus NS2
Analyse Structure of the catalytic domain of hepatitis C virus NS2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HD0
- Type
- protein
- Length
- 1,525 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease NS2-3 (P23)
- EC
- 3.4.22.-
- UniProt
- P27958
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I, J, K, L | Protease NS2-3 (P23) (EC 3.4.22.-) | protein | 127 | 32% helix, 16% strand | P27958 |
| H | Protease NS2-3 (P23) (EC 3.4.22.-) | protein | 128 | 30% helix, 15% strand | P27958 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 11 copies · chains A, E, C, B, F, D, H, J, L, I, K, G
- DMU · Decyl-beta-D-maltopyranoside · additive · chains G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.74 | 0.80 | 72 | BOG |
| 2 | 984 | 0.73 | 0.76 | 62 | BOG |
| 3 | 699 | 0.69 | 0.76 | 51 | BOG |
| 4 | 610 | 0.67 | 0.76 | 48 | BOG |
| 5 | 344 | 0.62 | 0.78 | 34 | BOG |
Interfaces
28 interfaces between chains.
- C–D · 2235 Ų buried · 34 hydrogen bonds · protein-protein
- K–L · 2228 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 2225 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2225 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2221 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2HD0 · Structure of the catalytic domain of hepatitis C virus NS2 · the same entry in another collection · chain E against E, 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 P27958
- Elsewhere: RCSB PDB 2HD0 · PDBe 2HD0 · UniProt P27958
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