Research workbench
Cetuximab Fab in complex with L5Y meditope variant
Analyse Cetuximab Fab in complex with L5Y meditope variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F88
- Type
- protein
- Length
- 880 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; L5Y meditope
- Ligands
- NAG, PO4
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| B | Cetuximab Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| E, F | L5Y meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.73 | 0.77 | 102 | empty |
| 2 | 405 | 0.63 | 0.78 | 48 | PO4 |
| 3 | 381 | 0.61 | 0.77 | 45 | PO4 |
| 4 | 284 | 0.57 | 0.77 | 54 | empty |
| 5 | 173 | 0.46 | 0.75 | 30 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1731 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1694 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 753 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 523 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 523 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5F88 · Cetuximab Fab in complex with L5Y meditope variant · 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
- Elsewhere: RCSB PDB 5F88 · PDBe 5F88
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