MolNFT v1 · #31048 · protein
Crystal structure of ERBB4/HER4 extracellular domain
2AHX · Receptor tyrosine-protein kinase erbb-4: “Crystal structure of ERBB4/HER4 extracellular domain”. X-ray diffraction, 3 ligands (NAG, YT3, SO4), 9 pockets (best druggability 0.48). MolNFT v1 #31048 on GenesisL1: 3D structure, binding…
- PDB
- 2AHX
- Type
- protein
- Length
- 1,226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-4
- EC
- 2.7.1.112
- UniProt
- Q15303
- Ligands
- NAG, YT3, SO4
- Pockets
- 9 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.1.112) | protein | 611 | 11% helix, 28% strand | Q15303 |
| B | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.1.112) | protein | 615 | 12% helix, 28% strand | Q15303 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.48 | 0.76 | 24 | empty |
| 2 | 50 | 0.48 | 0.86 | 14 | empty |
| 3 | 108 | 0.44 | 0.78 | 26 | NAG |
| 4 | 89 | 0.40 | 0.78 | 19 | empty |
| 5 | 94 | 0.39 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 2AHX · Crystal structure of ErbB4/HER4 extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q15303 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-4 (Q15303) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q15303
- Elsewhere: RCSB PDB 2AHX · PDBe 2AHX · UniProt Q15303
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