MolNFT v1 · #27465 · protein
Crystal structure of salicylic acid-binding protein 2 (SABP2) from nicotiana tabacum, nesg target AR2241
1XKL: “Crystal structure of salicylic acid-binding protein 2 (SABP2) from nicotiana tabacum, nesg target AR2241”. X-ray diffraction, 1 ligand (STH), 10 pockets (best druggability 0.62). MolNFT v1 #27465 on GenesisL1: 3D structure, binding…
- PDB
- 1XKL
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylic acid-binding protein 2
- UniProt
- Q6RYA0
- Ligands
- STH
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Salicylic acid-binding protein 2 | protein | 258 | 41% helix, 16% strand | Q6RYA0 |
| B | Salicylic acid-binding protein 2 | protein | 256 | 41% helix, 17% strand | Q6RYA0 |
| C | Salicylic acid-binding protein 2 | protein | 257 | 42% helix, 17% strand | Q6RYA0 |
| D | Salicylic acid-binding protein 2 | protein | 257 | 41% helix, 16% strand | Q6RYA0 |
Ligands and binding sites
- STH · 2-amino-4H-1,3-benzoxathiin-4-ol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.62 | 0.81 | 27 | empty |
| 2 | 148 | 0.52 | 0.80 | 37 | empty |
| 3 | 166 | 0.48 | 0.77 | 19 | empty |
| 4 | 59 | 0.40 | 0.80 | 17 | empty |
| 5 | 134 | 0.39 | 0.74 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 874 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 856 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 636 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 1XKL · Crystal Structure of Salicylic Acid-binding Protein 2 (SABP2) from Nicotiana tabacum… · the same entry in another collection · chain D against D, 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 A 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 1XKL · PDBe 1XKL · UniProt Q6RYA0
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