Research workbench
Structural and biochemical studies identify tobacco SABP2 as a methylsalicylate esterase and further implicate it in plant innate immunity, northeast structural genomics target AR2241
Analyse Structural and biochemical studies identify tobacco SABP2 as a methylsalicylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y7H
- Type
- protein
- Length
- 2,064 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylic acid-binding protein 2
- UniProt
- Q6RYA0
- Ligands
- SCN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Salicylic acid-binding protein 2 | protein | 257 | 39% helix, 18% strand | Q6RYA0 |
| B, D, H | Salicylic acid-binding protein 2 | protein | 259 | 39% helix, 15% strand | Q6RYA0 |
| E | Salicylic acid-binding protein 2 | protein | 258 | 41% helix, 17% strand | Q6RYA0 |
| F | Salicylic acid-binding protein 2 | protein | 258 | 39% helix, 16% strand | Q6RYA0 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.75 | 0.79 | 87 | empty |
| 2 | 923 | 0.74 | 0.77 | 114 | empty |
| 3 | 57 | 0.72 | 0.98 | 18 | empty |
| 4 | 57 | 0.71 | 0.97 | 23 | empty |
| 5 | 53 | 0.71 | 0.98 | 19 | empty |
Interfaces
9 interfaces between chains.
- G–H · 879 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 860 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 851 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 845 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 580 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 1Y7H · Structural and biochemical studies identify tobacco SABP2 as a methylsalicylate esterase… · the same entry in another collection · chain H against H, TM-score 1.00
- Q6RYA0 · AlphaFold monomer V2.0 prediction for salicylic acid-binding protein 2 (Q6RYA0) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q6RYA0
- Elsewhere: RCSB PDB 1Y7H · PDBe 1Y7H · UniProt Q6RYA0
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