MolNFT v1 · #140411 · protein
Crystal 1 for ATLURE1.2-ATPRK6LRR
5Y9W · Pollen receptor-like kinase 6: “Crystal 1 for ATLURE1.2-ATPRK6LRR”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.48). MolNFT v1 #140411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y9W
- Type
- protein
- Length
- 466 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pollen receptor-like kinase 6; Protein lure 1.2
- UniProt
- Q3E991, Q4VP08
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pollen receptor-like kinase 6 | protein | 216 | 17% helix, 26% strand | Q3E991 |
| C | Protein lure 1.2 | protein | 37 | 38% helix, 24% strand | Q4VP08 |
| A | Pollen receptor-like kinase 6 | protein | 213 | 17% helix, 22% strand | Q3E991 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.48 | 0.75 | 26 | empty |
| 2 | 81 | 0.32 | 0.74 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 679 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 276 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5Y9W · Crystal 1 for AtLURE1.2-AtPRK6LRR · the same entry in another collection · chain B against B, TM-score 1.00
- Q4VP08 · AlphaFold monomer V2.0 prediction for protein lure 1.2 (Q4VP08) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q3E991 · AlphaFold monomer V2.0 prediction for pollen receptor-like kinase 6 (Q3E991) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q3E991
- Every structure of UniProt Q4VP08
- Elsewhere: RCSB PDB 5Y9W · PDBe 5Y9W · UniProt Q3E991 · UniProt Q4VP08
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