Research workbench
Structure of cetuximab Fab with cyclic F3Q variant of the meditope
Analyse Structure of cetuximab Fab with cyclic F3Q variant of the meditope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2I
- Type
- protein
- Length
- 886 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; Meditope
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.72
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 | 6% helix, 50% strand | — |
| B | Cetuximab Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 216 | 7% helix, 51% strand | — |
| E, F | Meditope | protein | 12 | 0% helix, 50% strand | — |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.72 | 0.76 | 89 | empty |
| 2 | 390 | 0.63 | 0.78 | 47 | PO4 |
| 3 | 370 | 0.61 | 0.77 | 46 | PO4 |
| 4 | 262 | 0.54 | 0.76 | 59 | empty |
| 5 | 238 | 0.52 | 0.76 | 42 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1880 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1762 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 510 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 504 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5I2I · Structure of cetuximab Fab with cyclic F3Q variant of the meditope · 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 5I2I · PDBe 5I2I
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