Research workbench
Three dimensional structure of broadly neutralizing human anti - hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-1
Analyse Three dimensional structure of broadly neutralizing human anti - hepatitis C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZN
- Type
- protein
- Length
- 1,280 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HCV E2 Fab HC84-1 heavy chain; Anti-HCV E2 Fab HC84-1 light chain; Envelope…
- UniProt
- P27958
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-HCV E2 Fab HC84-1 heavy chain | protein | 212 | 6% helix, 52% strand | — |
| B | Anti-HCV E2 Fab HC84-1 light chain | protein | 213 | 7% helix, 50% strand | — |
| C | Anti-HCV E2 Fab HC84-1 heavy chain | protein | 203 | 6% helix, 51% strand | — |
| D | Anti-HCV E2 Fab HC84-1 light chain | protein | 212 | 7% helix, 50% strand | — |
| I | Anti-HCV E2 Fab HC84-1 heavy chain | protein | 215 | 6% helix, 53% strand | — |
| K | Envelope glycoprotein E2 | protein | 12 | 0% helix, 0% strand | P27958 |
| P | Anti-HCV E2 Fab HC84-1 light chain | protein | 213 | 7% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains K, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.77 | 0.80 | 114 | empty |
| 2 | 400 | 0.67 | 0.80 | 66 | empty |
| 3 | 677 | 0.66 | 0.75 | 60 | empty |
| 4 | 82 | 0.60 | 0.88 | 18 | empty |
| 5 | 293 | 0.60 | 0.78 | 40 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1779 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1762 Ų buried · 17 hydrogen bonds · protein-protein
- I–P · 1726 Ų buried · 17 hydrogen bonds · protein-protein
- C–P · 516 Ų buried · 7 hydrogen bonds · protein-protein
- B–I · 453 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4JZN · Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)… · 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 P27958
- Elsewhere: RCSB PDB 4JZN · PDBe 4JZN · UniProt P27958
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