Research workbench
Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana AT3G16990
Analyse Ensemble refinement of the protein crystal structure of gene product from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q4X
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seed maturation protein PM36 homolog
- UniProt
- Q9ASY9
- Ligands
- HMH, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seed maturation protein PM36 homolog | protein | 215 | 71% helix, 3% strand | Q9ASY9 |
| B | Seed maturation protein PM36 homolog | protein | 211 | 79% helix, 0% strand | Q9ASY9 |
Ligands and binding sites
- HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.65 | 0.89 | 23 | HMH |
| 2 | 122 | 0.63 | 0.86 | 22 | HMH |
| 3 | 159 | 0.61 | 0.84 | 22 | empty |
| 4 | 60 | 0.34 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 8 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 2Q4X · Ensemble refinement of the protein crystal structure of gene product from Arabidopsis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ASY9 · AlphaFold monomer V2.0 prediction for bifunctional tena-E protein (Q9ASY9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9ASY9
- Elsewhere: RCSB PDB 2Q4X · PDBe 2Q4X · UniProt Q9ASY9
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