Research workbench
X-ray structure of galt-like protein from arabidopsis thaliana AT5G18200
Analyse X-ray structure of galt-like protein from arabidopsis thaliana AT5G18200 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z84
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-1-phosphate uridyl transferase-like protein
- UniProt
- Q9FK51
- Ligands
- AMP, ZN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactose-1-phosphate uridyl transferase-like protein | protein | 311 | 32% helix, 24% strand | Q9FK51 |
| B | Galactose-1-phosphate uridyl transferase-like protein | protein | 305 | 31% helix, 25% strand | Q9FK51 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.84 | 0.86 | 99 | EDO, AMP |
| 2 | 150 | 0.54 | 0.80 | 30 | AMP |
| 3 | 52 | 0.34 | 0.78 | 13 | empty |
| 4 | 52 | 0.30 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2013 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1Z84 · X-ray structure of galt-like protein from arabidopsis thaliana at5g18200 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9FK51 · AlphaFold monomer V2.0 prediction for ADP-glucose phosphorylase (Q9FK51) · 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 Q9FK51
- Elsewhere: RCSB PDB 1Z84 · PDBe 1Z84 · UniProt Q9FK51
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