Research workbench
Fab fragments of chikungunya virus neutralizing human monoclonal antibody 5M16
Analyse Fab fragments of chikungunya virus neutralizing human monoclonal antibody 5M16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CHN
- Type
- protein
- Length
- 865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 5M16 Fab heavy chain; Antibody 5M16 Fab light chain
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 5M16 Fab heavy chain | protein | 215 | 11% helix, 52% strand | — |
| L, B | Antibody 5M16 Fab light chain | protein | 218 | 5% helix, 50% strand | — |
| A | Antibody 5M16 Fab heavy chain | protein | 214 | 9% helix, 51% strand | — |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.75 | 0.78 | 97 | empty |
| 2 | 250 | 0.54 | 0.77 | 35 | empty |
| 3 | 331 | 0.54 | 0.74 | 43 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1675 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1665 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 327 Ų buried · 5 hydrogen bonds · protein-protein
- L–B · 121 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5CHN · Fab fragments of chikungunya virus neutralizing human monoclonal antibody 5M16 · 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 5CHN · PDBe 5CHN
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