Research workbench
Crystal structure of plant peptide RALF23 in complex with fer and LLG2
Analyse Crystal structure of plant peptide RALF23 in complex with fer and LLG2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A5E
- Type
- protein
- Length
- 948 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-like protein kinase feronia; Gpi-anchored protein LLG2; RALF23
- EC
- 2.7.11.1
- UniProt
- Q9SCZ4, Q6NLF4
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Receptor-like protein kinase feronia (EC 2.7.11.1) | protein | 375 | 8% helix, 38% strand | Q9SCZ4 |
| C, D | Gpi-anchored protein LLG2 | protein | 84 | 49% helix, 1% strand | Q6NLF4 |
| E, F | RALF23 | protein | 15 | 47% helix, 7% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.77 | 0.82 | 63 | empty |
| 2 | 625 | 0.76 | 0.82 | 61 | empty |
| 3 | 98 | 0.59 | 0.87 | 25 | empty |
| 4 | 86 | 0.56 | 0.86 | 17 | empty |
| 5 | 350 | 0.52 | 0.73 | 37 | empty |
Interfaces
9 interfaces between chains.
- C–E · 971 Ų buried · 17 hydrogen bonds · protein-protein
- F–D · 959 Ų buried · 15 hydrogen bonds · protein-protein
- D–B · 582 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 329 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6A5E · Crystal structure of plant peptide RALF23 in complex with FER and LLG2 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9SCZ4 · AlphaFold monomer V2.0 prediction for receptor-like protein kinase feronia (Q9SCZ4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6NLF4 · AlphaFold monomer V2.0 prediction for gpi-anchored protein LLG2 (Q6NLF4) · a predicted model of the same protein · chain C 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 Q9SCZ4
- Every structure of UniProt Q6NLF4
- Elsewhere: RCSB PDB 6A5E · PDBe 6A5E · UniProt Q9SCZ4 · UniProt Q6NLF4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.