MolNFT v1 · #120153 · protein
Crystal structure of PEPR1-ATPEP1
5GR8 · Leucine-rich repeat receptor-like protein kinase PEPR1: “Crystal structure of PEPR1-ATPEP1”. X-ray diffraction, 2 ligands (NAG, SO4), 5 pockets (best druggability 0.57). MolNFT v1 #120153 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GR8
- Type
- protein
- Length
- 1,453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat receptor-like protein kinase PEPR1; Elicitor peptide 1
- EC
- 2.7.11.1
- UniProt
- Q9SSL9, Q9LV87
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Leucine-rich repeat receptor-like protein kinase PEPR1 (EC 2.7.11.1) | protein | 710 | 18% helix, 23% strand | Q9SSL9 |
| J | Elicitor peptide 1 | protein | 17 | 0% helix, 0% strand | Q9LV87 |
| P | Elicitor peptide 1 | protein | 16 | 0% helix, 0% strand | Q9LV87 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, J, D, P
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.57 | 0.75 | 46 | empty |
| 2 | 61 | 0.44 | 0.83 | 13 | empty |
| 3 | 92 | 0.41 | 0.78 | 25 | empty |
| 4 | 61 | 0.29 | 0.74 | 22 | empty |
| 5 | 51 | 0.25 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–J · 1113 Ų buried · 23 hydrogen bonds · protein-protein
- D–P · 972 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 197 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5GR8 · Crystal structure of PEPR1-AtPEP1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SSL9 · AlphaFold monomer V2.0 prediction for leucine-rich repeat receptor- like protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q9LV87 · AlphaFold monomer V2.0 prediction for elicitor peptide 1 (Q9LV87) · a predicted model of the same protein · chain P against A, TM-score 0.29
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 Q9SSL9
- Every structure of UniProt Q9LV87
- Elsewhere: RCSB PDB 5GR8 · PDBe 5GR8 · UniProt Q9SSL9 · UniProt Q9LV87
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