MolNFT v1 · #120993 · protein
Structure of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) showing X-ray induced reduction of plp internal aldimine to 4'-deoxy-piridoxine-phosphate (plr)
5HHY · Serine--pyruvate aminotransferase: “Structure of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) showing X-ray induced reduction…”. X-ray diffraction, 1 ligand (PLR), 3 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 5HHY
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--pyruvate aminotransferase
- EC
- 2.6.1.51, 2.6.1.44
- UniProt
- P21549
- Ligands
- PLR
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 385 | 42% helix, 16% strand | P21549 |
| B | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 386 | 42% helix, 16% strand | P21549 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.68 | 0.82 | 46 | PLR |
| 2 | 356 | 0.66 | 0.80 | 47 | PLR |
| 3 | 96 | 0.34 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4085 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5HHY · Structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) showing… · the same entry in another collection · chain A against A, TM-score 1.00
- P21549 · AlphaFold monomer V2.0 prediction for serine--pyruvate aminotransferase (P21549) · 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 P21549
- Elsewhere: RCSB PDB 5HHY · PDBe 5HHY · UniProt P21549
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