MolNFT v1 · #120388 · protein
Plant receptor complex
5GYY · S-receptor kinase SRK9: “Plant receptor complex”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.84). MolNFT v1 #120388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GYY
- Type
- protein
- Length
- 917 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-receptor kinase SRK9; S-locus protein 11
- UniProt
- Q7DN95, Q9ST12
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-receptor kinase SRK9 | protein | 400 | 7% helix, 43% strand | Q7DN95 |
| B | S-receptor kinase SRK9 | protein | 405 | 6% helix, 43% strand | Q7DN95 |
| G | S-locus protein 11 | protein | 58 | 22% helix, 36% strand | Q9ST12 |
| H | S-locus protein 11 | protein | 54 | 24% helix, 39% strand | Q9ST12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.84 | 0.90 | 89 | empty |
| 2 | 1120 | 0.82 | 0.83 | 96 | empty |
| 3 | 85 | 0.49 | 0.82 | 17 | empty |
| 4 | 94 | 0.48 | 0.81 | 17 | empty |
| 5 | 152 | 0.47 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 971 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 774 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 751 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 453 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 448 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5GYY · Plant receptor complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7DN95
- Every structure of UniProt Q9ST12
- Elsewhere: RCSB PDB 5GYY · PDBe 5GYY · UniProt Q7DN95 · UniProt Q9ST12
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