Research workbench
Ligand-triggered allosteric ADP release primes a plant nlr complex
Analyse Ligand-triggered allosteric ADP release primes a plant nlr complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J5U
- Type
- protein
- Length
- 1,164 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disease resistance RPP13-like protein 4; Probable SERINE/THREONINE-protein kinase PBL2…
- EC
- 2.7.11.1
- UniProt
- Q38834, O49839, Q9SVY5
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 34% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disease resistance RPP13-like protein 4 | protein | 663 | 31% helix, 9% strand | Q38834 |
| C | Probable SERINE/THREONINE-protein kinase PBL2 (EC 2.7.11.1) | protein | 174 | 33% helix, 1% strand | O49839 |
| B | Protein kinase superfamily protein | protein | 327 | 41% helix, 12% strand | Q9SVY5 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.81 | 0.83 | 92 | empty |
| 2 | 632 | 0.76 | 0.82 | 60 | empty |
| 3 | 78 | 0.68 | 0.93 | 19 | empty |
| 4 | 350 | 0.68 | 0.81 | 42 | empty |
| 5 | 57 | 0.66 | 0.95 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1750 Ų buried · 18 hydrogen bonds · protein-protein
- C–B · 1290 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6J5U · Ligand-triggered allosteric ADP release primes a plant NLR complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q38834 · AlphaFold monomer V2.0 prediction for disease resistance RPP13-like protein 4 (Q38834) · a predicted model of the same protein · chain A against A, TM-score 0.97
- 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 0.96
- O49839 · AlphaFold monomer V2.0 prediction for probable SERINE/THREONINE- protein kinase PBL2… · a predicted model of the same protein · chain C against A, TM-score 0.88
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 Q38834
- Every structure of UniProt O49839
- Every structure of UniProt Q9SVY5
- Elsewhere: RCSB PDB 6J5U · PDBe 6J5U · UniProt Q38834 · UniProt O49839 · UniProt Q9SVY5
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