MolNFT v1 · #153177 · protein
Ligand-triggered allosteric ADP release primes a plant nlr complex
6J5V · Disease resistance RPP13-like protein 4: “Ligand-triggered allosteric ADP release primes a plant nlr complex”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #153177 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6J5V
- Type
- protein
- Length
- 1,317 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 0.79
Structure
electron microscopy · 3 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disease resistance RPP13-like protein 4 | protein | 816 | 30% 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 | 40% helix, 13% strand | Q9SVY5 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.79 | 0.98 | 21 | empty |
| 2 | 608 | 0.79 | 0.85 | 82 | empty |
| 3 | 110 | 0.77 | 0.96 | 32 | empty |
| 4 | 99 | 0.76 | 0.96 | 27 | empty |
| 5 | 590 | 0.73 | 0.80 | 62 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1699 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 1312 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6J5V · Ligand-triggered allosteric ADP release primes a plant NLR complex · the same entry in another collection · chain A against A, 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 0.96
- 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
- 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 0.83
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 6J5V · PDBe 6J5V · UniProt Q38834 · UniProt O49839 · UniProt Q9SVY5
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