Research workbench
Structure of cetuximab Fab mutant in complex with EGFR extracellular domain
Analyse Structure of cetuximab Fab mutant in complex with EGFR extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ARU
- Type
- protein
- Length
- 1,031 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Cetuximab mutant light CHAIN,UNCHARACTERIZED protein…
- EC
- 2.7.10.1
- UniProt
- P00533, Q8TCD0, P0DOX5
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 609 | 12% helix, 26% strand | P00533 |
| B | Cetuximab mutant light CHAIN,UNCHARACTERIZED protein | protein | 210 | 6% helix, 50% strand | Q8TCD0 |
| C | Cetuximab mutant heavy chain Fab FRAGMENT,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 212 | 7% helix, 52% strand | P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.51 | 0.77 | 36 | empty |
| 2 | 212 | 0.46 | 0.74 | 29 | empty |
| 3 | 160 | 0.46 | 0.76 | 33 | empty |
| 4 | 155 | 0.44 | 0.75 | 25 | empty |
| 5 | 120 | 0.42 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1709 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6ARU · Structure of Cetuximab Fab mutant in complex with EGFR extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P00533
- Every structure of UniProt Q8TCD0
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 6ARU · PDBe 6ARU · UniProt P00533 · UniProt Q8TCD0 · UniProt P0DOX5
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