Research workbench
Alanine-glyoxylate aminotransferase 1 (AGT1) from arabidopsis thaliana
Analyse Alanine-glyoxylate aminotransferase 1 (AGT1) from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PK3
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--glyoxylate aminotransferase
- EC
- 2.6.1.45, 2.6.1.44, 2.6.1.-, 2.6.1.51
- UniProt
- Q56YA5
- Ligands
- PLP, CL
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--glyoxylate aminotransferase (EC 2.6.1.45, 2.6.1.44, 2.6.1.-, 2.6.1.51) | protein | 399 | 44% helix, 17% strand | Q56YA5 |
| B | Serine--glyoxylate aminotransferase (EC 2.6.1.45, 2.6.1.44, 2.6.1.-, 2.6.1.51) | protein | 400 | 44% helix, 17% strand | Q56YA5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.70 | 0.89 | 35 | empty |
| 2 | 114 | 0.59 | 0.86 | 21 | empty |
| 3 | 257 | 0.58 | 0.79 | 38 | empty |
| 4 | 214 | 0.48 | 0.75 | 24 | empty |
| 5 | 73 | 0.45 | 0.81 | 17 | PLP |
Interfaces
1 interface between chains.
- A–B · 2610 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6PK3 · Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q56YA5 · AlphaFold monomer V2.0 prediction for serine--glyoxylate aminotransferase (Q56YA5) · a predicted model of the same protein · chain A 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 Q56YA5
- Elsewhere: RCSB PDB 6PK3 · PDBe 6PK3 · UniProt Q56YA5
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