Research workbench
Crystal structure of rituximab Fab in complex with an epitope peptide
Analyse Crystal structure of rituximab Fab in complex with an epitope peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OSL
- Type
- protein
- Length
- 913 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of the rituximab Fab FRAGMENT,LIGHT chain of the rituximab Fab fragment…
- UniProt
- P11836
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | Light chain of the rituximab Fab FRAGMENT,LIGHT chain of the rituximab Fab fragment | protein | 213 | 5% helix, 51% strand | — |
| H | Heavy chain of the rituximab Fab FRAGMENT,HEAVY chain of the rituximab Fab fragment | protein | 224 | 7% helix, 52% strand | — |
| A | Heavy chain of the rituximab Fab FRAGMENT,HEAVY chain of the rituximab Fab fragment | protein | 221 | 7% helix, 52% strand | — |
| P | B-lymphocyte antigen CD20 | protein | 20 | 50% helix, 0% strand | P11836 |
| Q | B-lymphocyte antigen CD20 | protein | 22 | 45% helix, 0% strand | P11836 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.69 | 0.79 | 61 | empty |
| 2 | 154 | 0.65 | 0.87 | 28 | empty |
| 3 | 83 | 0.54 | 0.86 | 22 | empty |
| 4 | 156 | 0.52 | 0.79 | 23 | empty |
| 5 | 130 | 0.52 | 0.81 | 31 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1953 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1839 Ų buried · 13 hydrogen bonds · protein-protein
- L–B · 529 Ų buried · 2 hydrogen bonds · protein-protein
- H–P · 447 Ų buried · 8 hydrogen bonds · protein-protein
- A–Q · 425 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 2OSL · Crystal structure of Rituximab Fab in complex with an epitope peptide · the same entry in another collection · chain Q against Q, 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 0.60
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 2OSL · PDBe 2OSL · UniProt P11836
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