MolNFT v1 · #118872 · protein
Cetuximab Fab in complex with L10Q meditope variant
5FF6 · Cetuximab Fab light chain: “Cetuximab Fab in complex with L10Q meditope variant”. X-ray diffraction, 2 ligands (NAG, PO4), 10 pockets (best druggability 0.74). MolNFT v1 #118872 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5FF6
- Type
- protein
- Length
- 884 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cetuximab Fab light chain; Cetuximab Fab heavy chain; L10Q meditope
- Ligands
- NAG, PO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cetuximab Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| B | Cetuximab Fab heavy chain | protein | 220 | 7% helix, 52% strand | — |
| D | Cetuximab Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| E, F | L10Q 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 · 8 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.74 | 0.77 | 103 | empty |
| 2 | 393 | 0.63 | 0.78 | 45 | PO4 |
| 3 | 398 | 0.62 | 0.77 | 45 | PO4 |
| 4 | 172 | 0.46 | 0.75 | 32 | PO4 |
| 5 | 133 | 0.46 | 0.78 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1852 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1691 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 727 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 537 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 513 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5FF6 · Cetuximab Fab in complex with L10Q 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 5FF6 · PDBe 5FF6
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