Research workbench
The plant peptide hormone receptor complex
Analyse The plant peptide hormone receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z61
- Type
- protein
- Length
- 1,593 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytosulfokine receptor 1; Somatic embryogenesis receptor kinase 2; Ptr-ile-ptr-thr-gln
- EC
- 2.7.11.1
- UniProt
- Q8LPB4, Q9XIC7
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytosulfokine receptor 1 (EC 2.7.11.1) | protein | 610 | 17% helix, 21% strand | Q8LPB4 |
| B | Phytosulfokine receptor 1 (EC 2.7.11.1) | protein | 603 | 17% helix, 23% strand | Q8LPB4 |
| C, D | Somatic embryogenesis receptor kinase 2 (EC 2.7.11.1) | protein | 185 | 22% helix, 19% strand | Q9XIC7 |
| P, Q | Ptr-ile-ptr-thr-gln | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, Q, C, B, P, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.66 | 0.78 | 55 | empty |
| 2 | 495 | 0.65 | 0.77 | 45 | empty |
| 3 | 450 | 0.63 | 0.77 | 36 | empty |
| 4 | 312 | 0.60 | 0.78 | 33 | empty |
| 5 | 254 | 0.55 | 0.77 | 34 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1022 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1018 Ų buried · 8 hydrogen bonds · protein-protein
- A–Q · 770 Ų buried · 16 hydrogen bonds · protein-protein
- B–P · 748 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 504 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 13 disulfide, 4 modified (N-glycosylation, disulfide, sulfation).
Compared structures
- 4Z61 · The plant peptide hormone receptor complex · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9XIC7 · AlphaFold monomer V2.0 prediction for somatic embryogenesis receptor kinase 2 (Q9XIC7) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q8LPB4 · AlphaFold monomer V2.0 prediction for phytosulfokine receptor 1 (Q8LPB4) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8LPB4
- Every structure of UniProt Q9XIC7
- Elsewhere: RCSB PDB 4Z61 · PDBe 4Z61 · UniProt Q8LPB4 · UniProt Q9XIC7
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