Research workbench
X-ray structure of gene product from arabidopsis thaliana AT1G53580
Analyse X-ray structure of gene product from arabidopsis thaliana AT1G53580 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GCU
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydroxyacylglutathione hydrolase 3
- EC
- 3.1.2.6
- UniProt
- Q9C8L4
- Ligands
- FE2, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative hydroxyacylglutathione hydrolase 3 (EC 3.1.2.6) | protein | 244 | 25% helix, 27% strand | Q9C8L4 |
| B, D | Putative hydroxyacylglutathione hydrolase 3 (EC 3.1.2.6) | protein | 237 | 26% helix, 28% strand | Q9C8L4 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.72 | 0.78 | 67 | EDO |
| 2 | 699 | 0.72 | 0.79 | 95 | EDO, FE2 |
| 3 | 707 | 0.72 | 0.78 | 83 | EDO |
| 4 | 675 | 0.69 | 0.76 | 55 | EDO |
| 5 | 268 | 0.58 | 0.78 | 31 | FE2 |
Interfaces
5 interfaces between chains.
- C–D · 910 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 716 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 659 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2GCU · X-Ray Structure of Gene Product from Arabidopsis Thaliana At1g53580 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9C8L4 · AlphaFold monomer V2.0 prediction for persulfide dioxygenase ETHE1 homolog, mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 1.00
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 Q9C8L4
- Elsewhere: RCSB PDB 2GCU · PDBe 2GCU · UniProt Q9C8L4
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