Research workbench
Crystal structure of the extracellular domain of the epidermal growth factor receptor in complex with an adnectin
Analyse Crystal structure of the extracellular domain of the epidermal growth factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QWQ
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Adnectin
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 613 | 11% helix, 27% strand | P00533 |
| B | Adnectin | protein | 100 | 0% helix, 59% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.60 | 0.79 | 47 | empty |
| 2 | 179 | 0.49 | 0.77 | 31 | empty |
| 3 | 127 | 0.45 | 0.77 | 20 | empty |
| 4 | 71 | 0.33 | 0.75 | 14 | empty |
| 5 | 61 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3QWQ · Crystal structure of the extracellular domain of the epidermal growth factor receptor in… · 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 0.98
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 3QWQ · PDBe 3QWQ · UniProt P00533
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