Research workbench
Crystal structure of chimeric antibody C2H7 Fab in complex with a CD20 peptide
Analyse Crystal structure of chimeric antibody C2H7 Fab in complex with a CD20 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BKY
- Type
- protein
- Length
- 456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The Fab fragment of chimeric 2H7, heavy chain; The Fab fragment of chimeric 2H7, light…
- UniProt
- P11836
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | The Fab fragment of chimeric 2H7, heavy chain | protein | 226 | 3% helix, 50% strand | — |
| L | The Fab fragment of chimeric 2H7, light chain | protein | 213 | 7% helix, 50% strand | — |
| P | B-lymphocyte antigen CD20 | protein | 17 | 0% helix, 0% strand | P11836 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.56 | 0.74 | 66 | empty |
| 2 | 77 | 0.34 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2135 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 432 Ų buried · 1 hydrogen bond · protein-protein
- L–P · 131 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3BKY · Crystal Structure of Chimeric Antibody C2H7 Fab in complex with a CD20 Peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P11836 · AlphaFold monomer V2.0 prediction for B-lymphocyte antigen CD20 (P11836) · a predicted model of the same protein · chain P against A, TM-score 0.41
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 P11836
- Elsewhere: RCSB PDB 3BKY · PDBe 3BKY · UniProt P11836
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