MolNFT v1 · #118910 · protein
Three dimensional structure of broadly neutralizing human anti - hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.4
5FGB · Anti-HCV E2 Fab HC84-1 light chain: “Three dimensional structure of broadly neutralizing human anti - hepatitis C virus (HCV) glycoprotein E2 Fab…”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 5FGB
- Type
- protein
- Length
- 862 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HCV E2 Fab HC84-1 light chain; Anti-HCV E2 Fab HC84-1 heavy chain; Genome polyprotein
- EC
- 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
- UniProt
- P27958
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-HCV E2 Fab HC84-1 light chain | protein | 213 | 7% helix, 51% strand | — |
| B | Anti-HCV E2 Fab HC84-1 light chain | protein | 212 | 6% helix, 51% strand | — |
| C | Anti-HCV E2 Fab HC84-1 heavy chain | protein | 215 | 7% helix, 54% strand | — |
| E | Anti-HCV E2 Fab HC84-1 heavy chain | protein | 213 | 7% helix, 54% strand | — |
| F | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 5 | 0% helix, 0% strand | P27958 |
| G | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 4 | 0% helix, 0% strand | P27958 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, F
- GOL · Glycerol · additive · 4 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.75 | 0.78 | 108 | GOL |
| 2 | 1196 | 0.75 | 0.78 | 102 | empty |
| 3 | 52 | 0.50 | 0.87 | 24 | GOL |
| 4 | 129 | 0.44 | 0.76 | 20 | empty |
| 5 | 92 | 0.34 | 0.74 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1822 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1697 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1137 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 402 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 347 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5FGB · 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 5FGB · PDBe 5FGB · UniProt P27958
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