Research workbench
Crystal structure of the epidermal growth factor receptor extracellular region in complex with epigen
Analyse Crystal structure of the epidermal growth factor receptor extracellular region… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WB8
- Type
- protein
- Length
- 1,073 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epigen
- EC
- 2.7.10.1
- UniProt
- P00533, Q6UW88
- Ligands
- NAG, BMA, MAN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 501 | 13% helix, 25% strand | P00533 |
| B | Epigen | protein | 32 | 0% helix, 25% strand | Q6UW88 |
| C | Epigen | protein | 36 | 0% helix, 44% strand | Q6UW88 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 504 | 12% helix, 23% strand | P00533 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, D, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.79 | 0.81 | 114 | empty |
| 2 | 1146 | 0.73 | 0.77 | 111 | empty |
| 3 | 490 | 0.72 | 0.81 | 50 | empty |
| 4 | 107 | 0.56 | 0.85 | 31 | empty |
| 5 | 188 | 0.44 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1045 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 742 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5WB8 · Crystal structure of the epidermal growth factor receptor extracellular region in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6UW88 · AlphaFold monomer V2.0 prediction for epigen (Q6UW88) · a predicted model of the same protein · chain C against A, TM-score 0.88
- 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 0.69
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 Q6UW88
- Elsewhere: RCSB PDB 5WB8 · PDBe 5WB8 · UniProt P00533 · UniProt Q6UW88
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.