Research workbench
Structure of hepatitis C virus envelope full-length glycoprotein 2 (EE2) from J6 genotype
Analyse Structure of hepatitis C virus envelope full-length glycoprotein 2 (EE2) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MWW
- Type
- protein
- Length
- 606 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein precursor EE2; 2A12 Fab heavy chain; 2A12 Fab light chain
- EC
- 2.7.7.48, 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- A0A2I6PIY1
- Ligands
- NAG, BMA
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Core protein precursor EE2 (EC 2.7.7.48, 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 169 | 6% helix, 28% strand | A0A2I6PIY1 |
| H | 2A12 Fab heavy chain | protein | 219 | 7% helix, 51% strand | — |
| L | 2A12 Fab light chain | protein | 218 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.57 | 0.74 | 43 | empty |
| 2 | 164 | 0.52 | 0.78 | 25 | empty |
| 3 | 54 | 0.49 | 0.87 | 20 | empty |
| 4 | 144 | 0.43 | 0.75 | 25 | empty |
| 5 | 139 | 0.43 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1886 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 508 Ų buried · 11 hydrogen bonds · protein-protein
- E–L · 120 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7MWW · Structure of hepatitis C virus envelope full-length glycoprotein 2 (eE2) from J6 genotype · 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 A0A2I6PIY1
- Elsewhere: RCSB PDB 7MWW · PDBe 7MWW · UniProt A0A2I6PIY1
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