Research workbench
Ensemble refinement of the protein crystal structure of spermidine synthase from arabidopsis thaliana gene AT1G23820
Analyse Ensemble refinement of the protein crystal structure of spermidine synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q41
- Type
- protein
- Length
- 1,150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase 1
- EC
- 2.5.1.16
- UniProt
- Q9ZUB3
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spermidine synthase 1 (EC 2.5.1.16) | protein | 290 | 31% helix, 28% strand | Q9ZUB3 |
| B, D | Spermidine synthase 1 (EC 2.5.1.16) | protein | 285 | 31% helix, 29% strand | Q9ZUB3 |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.82 | 0.99 | 22 | empty |
| 2 | 114 | 0.81 | 0.99 | 20 | empty |
| 3 | 293 | 0.76 | 0.88 | 56 | empty |
| 4 | 351 | 0.76 | 0.86 | 57 | empty |
| 5 | 68 | 0.72 | 0.97 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1919 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1840 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1003 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 145 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2Q41 · Ensemble refinement of the protein crystal structure of spermidine synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZUB3 · AlphaFold monomer V2.0 prediction for spermidine synthase 1 (Q9ZUB3) · a predicted model of the same protein · chain B 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 Q9ZUB3
- Elsewhere: RCSB PDB 2Q41 · PDBe 2Q41 · UniProt Q9ZUB3
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