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Unexpected structure for the N-terminal domain of hepatitis C virus envelope glycoprotein E1
Analyse Unexpected structure for the N-terminal domain of hepatitis C virus envelope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UOI
- Type
- protein
- Length
- 403 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- H9XGD6
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 65 | 22% helix, 45% strand | H9XGD6 |
| B | Genome polyprotein | protein | 72 | 21% helix, 40% strand | H9XGD6 |
| C | Genome polyprotein | protein | 51 | 24% helix, 45% strand | H9XGD6 |
| D | Genome polyprotein | protein | 69 | 17% helix, 42% strand | H9XGD6 |
| E | Genome polyprotein | protein | 71 | 15% helix, 48% strand | H9XGD6 |
| F | Genome polyprotein | protein | 75 | 20% helix, 37% strand | H9XGD6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, F, C, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.48 | 0.75 | 33 | empty |
| 2 | 70 | 0.29 | 0.73 | 16 | empty |
Interfaces
11 interfaces between chains.
- D–E · 1468 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1249 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 782 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 772 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 376 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4UOI · Unexpected structure for the N-terminal domain of Hepatitis C virus envelope glycoprotein… · 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 H9XGD6
- Elsewhere: RCSB PDB 4UOI · PDBe 4UOI · UniProt H9XGD6
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