MolNFT v1 · #111944 · protein
The plant peptide hormone receptor complex in arabidopsis
4Z64 · Phytosulfokine receptor 1: “The plant peptide hormone receptor complex in arabidopsis”. X-ray diffraction, 2 ligands (NAG, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #111944 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Z64
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytosulfokine receptor 1; Somatic embryogenesis receptor kinase 1; Phytosulfokine
- EC
- 2.7.11.1, 2.7.10.1
- UniProt
- Q9ZVR7, Q94AG2
- Ligands
- NAG, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytosulfokine receptor 1 (EC 2.7.11.1) | protein | 605 | 18% helix, 22% strand | Q9ZVR7 |
| C | Somatic embryogenesis receptor kinase 1 (EC 2.7.10.1, 2.7.11.1) | protein | 186 | 21% helix, 24% strand | Q94AG2 |
| P | Phytosulfokine | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, P, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.71 | 0.81 | 49 | empty |
| 2 | 367 | 0.62 | 0.78 | 39 | empty |
| 3 | 370 | 0.54 | 0.74 | 34 | empty |
| 4 | 229 | 0.49 | 0.75 | 38 | SO4 |
Interfaces
2 interfaces between chains.
- A–C · 1019 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 768 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 7 disulfide, 2 modified (N-glycosylation, disulfide, sulfation).
Compared structures
- 4Z64 · the plant peptide hormone receptor complex in arabidopsis · the same entry in another collection · chain P against P, 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
- Q9ZVR7 · AlphaFold monomer V2.0 prediction for phytosulfokine receptor 1 (Q9ZVR7) · 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 Q9ZVR7
- Every structure of UniProt Q94AG2
- Elsewhere: RCSB PDB 4Z64 · PDBe 4Z64 · UniProt Q9ZVR7 · UniProt Q94AG2
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