MolNFT v1 · #122753 · protein
Crystal structure of the arabidopsis receptor kinase haesa in complex with the peptide hormone ida and the co-receptor SERK1
5IYX · Receptor-like protein kinase 5: “Crystal structure of the arabidopsis receptor kinase haesa in complex with the peptide hormone ida and the…”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.66). MolNFT v1 #122753…
- PDB
- 5IYX
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-like protein kinase 5; Protein ida; Somatic embryogenesis receptor kinase 1
- EC
- 2.7.10.1, 2.7.11.1
- UniProt
- P47735, Q8LAD7, Q94AG2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-like protein kinase 5 (EC 2.7.10.1, 2.7.11.1) | protein | 596 | 17% helix, 24% strand | P47735 |
| B | Protein ida | protein | 14 | 0% helix, 7% strand | Q8LAD7 |
| C | Somatic embryogenesis receptor kinase 1 (EC 2.7.10.1, 2.7.11.1) | protein | 186 | 24% helix, 25% strand | Q94AG2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.66 | 0.78 | 41 | empty |
| 2 | 273 | 0.62 | 0.80 | 40 | empty |
| 3 | 221 | 0.55 | 0.78 | 30 | empty |
| 4 | 101 | 0.40 | 0.77 | 26 | empty |
| 5 | 69 | 0.27 | 0.72 | 22 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide, 1 modified (N-glycosylation, disulfide, hydroxylation).
Compared structures
- 5IYX · Crystal structure of the Arabidopsis receptor kinase HAESA in complex with the peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q94AG2 · AlphaFold monomer V2.0 prediction for somatic embryogenesis receptor kinase 1 (Q94AG2) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P47735 · AlphaFold monomer V2.0 prediction for receptor-like protein kinase 5 (P47735) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8LAD7 · AlphaFold monomer V2.0 prediction for protein ida (Q8LAD7) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 P47735
- Every structure of UniProt Q8LAD7
- Every structure of UniProt Q94AG2
- Elsewhere: RCSB PDB 5IYX · PDBe 5IYX · UniProt P47735 · UniProt Q8LAD7 · UniProt Q94AG2
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