MolNFT v1 · #138188 · protein
Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin
5WB7: “Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.80). MolNFT v1 #138188 on GenesisL1: 3D…
- 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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