Research workbench
Crystal structure of Fab C2 in complex with a cyclic variant of hepatitis C virus E2 epitope I
Analyse Crystal structure of Fab C2 in complex with a cyclic variant of hepatitis C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EOC
- Type
- protein
- Length
- 883 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment (heavy chain); Fab fragment (light chain)…
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab fragment (heavy chain) | protein | 212 | 8% helix, 51% strand | — |
| L | Fab fragment (light chain) | protein | 216 | 6% helix, 53% strand | — |
| J | Fab fragment (heavy chain) | protein | 214 | 7% helix, 52% strand | — |
| M | Fab fragment (light chain) | protein | 215 | 6% helix, 51% strand | — |
| P, Q | Ala-cys-gln-leu-ile-asn-thr-asn-gly-ser-TRP-his-ile-cys | protein | 13 | 0% helix, 46% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.78 | 0.81 | 114 | empty |
| 2 | 1126 | 0.76 | 0.78 | 108 | empty |
| 3 | 95 | 0.34 | 0.74 | 24 | empty |
| 4 | 89 | 0.33 | 0.74 | 17 | empty |
Interfaces
9 interfaces between chains.
- J–M · 1834 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1822 Ų buried · 17 hydrogen bonds · protein-protein
- L–P · 374 Ų buried · 2 hydrogen bonds · protein-protein
- M–Q · 350 Ų buried · 1 hydrogen bond · protein-protein
- H–M · 275 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5EOC · Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 5EOC · PDBe 5EOC
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