MolNFT v1 · #69069 · protein
Crystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3 (HER3)
3KEX · Receptor tyrosine-protein kinase erbb-3: “Crystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3…”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.69).…
- PDB
- 3KEX
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3
- EC
- 2.7.10.1
- UniProt
- P21860
- Ligands
- ANP, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 292 | 30% helix, 17% strand | P21860 |
| B | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 283 | 32% helix, 18% strand | P21860 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.69 | 0.84 | 35 | ANP, MG |
| 2 | 312 | 0.68 | 0.82 | 40 | ANP, MG |
| 3 | 221 | 0.62 | 0.82 | 25 | empty |
| 4 | 467 | 0.59 | 0.74 | 60 | empty |
| 5 | 137 | 0.57 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3KEX · Crystal structure of the catalytically inactive kinase domain of the human epidermal… · the same entry in another collection · chain A against A, TM-score 1.00
- P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P21860
- Elsewhere: RCSB PDB 3KEX · PDBe 3KEX · UniProt P21860
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