Research workbench
Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of CETUXIMAB/ERBITUX/IMC- C225
Analyse Structure of the extracellular domain of the epidermal growth factor receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YY9
- Type
- protein
- Length
- 1,044 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Cetuximab Fab light chain; Cetuximab Fab heavy chain
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 613 | 13% helix, 25% strand | P00533 |
| C | Cetuximab Fab light chain | protein | 211 | 0% helix, 50% strand | — |
| D | Cetuximab Fab heavy chain | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 6 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
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.51 | 0.77 | 36 | empty |
| 2 | 211 | 0.44 | 0.73 | 34 | empty |
| 3 | 132 | 0.44 | 0.77 | 17 | empty |
| 4 | 128 | 0.42 | 0.75 | 23 | empty |
| 5 | 108 | 0.38 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1681 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 643 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 403 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 1YY9 · Structure of the extracellular domain of the epidermal growth factor receptor in complex… · 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
- Elsewhere: RCSB PDB 1YY9 · PDBe 1YY9 · UniProt P00533
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