Research workbench
Reconstitution and structure of a plant nlr resistosome conferring immunity
Analyse Reconstitution and structure of a plant nlr resistosome conferring immunity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J6I
- Type
- protein
- Length
- 4,472 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase PBL2; Protein kinase superfamily protein…
- EC
- 2.7.11.1
- UniProt
- O49839, Q9SVY5, Q38834
- Ligands
- DTP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase PBL2 (EC 2.7.11.1) | protein | 195 | 35% helix, 2% strand | O49839 |
| B | Protein kinase superfamily protein | protein | 327 | 39% helix, 15% strand | Q9SVY5 |
| C, F, G, L, O | Disease resistance RPP13-like protein 4 | protein | 790 | 35% helix, 13% strand | Q38834 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 5 copies · chains C, F, G, L, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.84 | 0.87 | 80 | DTP |
| 2 | 771 | 0.83 | 0.86 | 84 | DTP |
| 3 | 685 | 0.83 | 0.87 | 74 | DTP |
| 4 | 661 | 0.82 | 0.87 | 71 | DTP |
| 5 | 619 | 0.82 | 0.87 | 67 | DTP |
Interfaces
12 interfaces between chains.
- C–G · 2512 Ų buried · 24 hydrogen bonds · protein-protein
- F–L · 2494 Ų buried · 24 hydrogen bonds · protein-protein
- C–F · 2488 Ų buried · 24 hydrogen bonds · protein-protein
- L–O · 2472 Ų buried · 24 hydrogen bonds · protein-protein
- G–O · 2471 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6J6I · Reconstitution and structure of a plant NLR resistosome conferring immunity · the same entry in another collection · chain O against O, TM-score 1.00
- Q9SVY5 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase ZRK1 (Q9SVY5) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O49839 · AlphaFold monomer V2.0 prediction for probable SERINE/THREONINE- protein kinase PBL2… · a predicted model of the same protein · chain A against A, TM-score 0.86
- Q38834 · AlphaFold monomer V2.0 prediction for disease resistance RPP13-like protein 4 (Q38834) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 O49839
- Every structure of UniProt Q9SVY5
- Every structure of UniProt Q38834
- Elsewhere: RCSB PDB 6J6I · PDBe 6J6I · UniProt O49839 · UniProt Q9SVY5 · UniProt Q38834
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