Research workbench
Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin
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
- 5WB7
- Type
- protein
- Length
- 2,186 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Proepiregulin
- EC
- 2.7.10.1
- UniProt
- P00533, O14944
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 500 | 13% helix, 23% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 504 | 14% helix, 24% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 499 | 14% helix, 23% strand | P00533 |
| E, G | Proepiregulin | protein | 47 | 6% helix, 40% strand | O14944 |
| F | Proepiregulin | protein | 45 | 0% helix, 42% strand | O14944 |
| H | Proepiregulin | protein | 44 | 0% helix, 43% strand | O14944 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, G, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.82 | 107 | empty |
| 2 | 1017 | 0.80 | 0.82 | 94 | empty |
| 3 | 829 | 0.78 | 0.81 | 91 | empty |
| 4 | 849 | 0.73 | 0.77 | 92 | empty |
| 5 | 489 | 0.72 | 0.81 | 62 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1508 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1359 Ų buried · 20 hydrogen bonds · protein-protein
- C–G · 1237 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1138 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1125 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 5WB7 · Crystal structure of the epidermal growth factor receptor extracellular region in complex… · the same entry in another collection · chain H against H, TM-score 1.00
- O14944 · AlphaFold monomer V2.0 prediction for proepiregulin (O14944) · a predicted model of the same protein · chain H against A, TM-score 0.91
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 O14944
- Elsewhere: RCSB PDB 5WB7 · PDBe 5WB7 · UniProt P00533 · UniProt O14944
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