Research workbench
Cryo-EM structure of the extracellular module of the full-length EGFR bound to EGF "tips-juxtaposed" conformation
Analyse Cryo-EM structure of the extracellular module of the full-length EGFR bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SYD
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epidermal growth factor
- EC
- 2.7.10.1
- UniProt
- P00533, P01133
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 8% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 614 | 8% helix, 23% strand | P00533 |
| C, D | Epidermal growth factor | protein | 47 | 6% helix, 30% strand | P01133 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.82 | 0.84 | 98 | empty |
| 2 | 499 | 0.73 | 0.82 | 59 | empty |
| 3 | 408 | 0.71 | 0.82 | 53 | empty |
| 4 | 208 | 0.59 | 0.81 | 32 | empty |
| 5 | 206 | 0.59 | 0.81 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1561 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1555 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1546 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide (disulfide).
Compared structures
- 7SYD · Cryo-EM structure of the extracellular module of the full-length EGFR bound to EGF… · the same entry in another collection · chain D against D, TM-score 1.00
- P01133 · AlphaFold monomer V2.0 prediction for pro-epidermal growth factor (P01133) · a predicted model of the same protein · chain C against A, TM-score 0.80
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain B against A, TM-score 0.53
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 P01133
- Elsewhere: RCSB PDB 7SYD · PDBe 7SYD · UniProt P00533 · UniProt P01133
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