MolNFT v1 · #48822 · protein
Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana AT3G16990
2Q4X · Seed maturation protein PM36 homolog: “Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana AT3G16990”. X-ray diffraction, 2 ligands (HMH, SO4), 4 pockets (best druggability 0.65). MolNFT v1…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.