Research workbench
Crystal structure of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of imc-11F8
Analyse Crystal structure of the extracellular region 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
- 3B2V
- Type
- protein
- Length
- 805 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imc-11F8 Fab light chain; Imc-11F8 Fab heavy chain; Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, BMA
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Imc-11F8 Fab light chain | protein | 213 | 2% helix, 30% strand | — |
| H | Imc-11F8 Fab heavy chain | protein | 217 | 3% helix, 40% strand | — |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 375 | 6% helix, 15% strand | P00533 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.63 | 0.81 | 46 | empty |
| 2 | 61 | 0.60 | 0.91 | 26 | empty |
| 3 | 156 | 0.58 | 0.82 | 28 | empty |
| 4 | 99 | 0.57 | 0.85 | 28 | empty |
| 5 | 415 | 0.55 | 0.73 | 54 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1382 Ų buried · 5 hydrogen bonds · protein-protein
- H–A · 595 Ų buried · 5 hydrogen bonds · protein-protein
- L–A · 348 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3B2V · Crystal structure of the extracellular region of the epidermal growth factor receptor in… · the same entry in another collection · chain L against L, 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 0.94
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 3B2V · PDBe 3B2V · UniProt P00533
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