Research workbench
Structure of spermidine disinapoyl TRANSFERASES(SDT) from arabidopsis thaliana
Analyse Structure of spermidine disinapoyl TRANSFERASES(SDT) from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LPW
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine sinapoyl-CoA acyltransferase
- EC
- 2.3.1.248
- UniProt
- O80467
- Ligands
- SPD
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine sinapoyl-CoA acyltransferase (EC 2.3.1.248) | protein | 431 | 34% helix, 25% strand | O80467 |
| B | Spermidine sinapoyl-CoA acyltransferase (EC 2.3.1.248) | protein | 436 | 32% helix, 25% strand | O80467 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.87 | 0.88 | 108 | empty |
| 2 | 578 | 0.82 | 0.87 | 54 | SPD |
| 3 | 409 | 0.67 | 0.79 | 47 | empty |
| 4 | 142 | 0.53 | 0.81 | 29 | empty |
| 5 | 139 | 0.51 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6LPW · Structure of Spermidine disinapoyl transferases(SDT) from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- O80467 · AlphaFold monomer V2.0 prediction for spermidine sinapoyl-CoA acyltransferase (O80467) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O80467
- Elsewhere: RCSB PDB 6LPW · PDBe 6LPW · UniProt O80467
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