MolNFT v1 · #118694 · protein
Crystal structure of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) at 1.7 ångström; internal aldimine with plp in the active site
5F9S · Serine--pyruvate aminotransferase: “Crystal structure of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) at 1.7 ångström…”. X-ray diffraction, 1 ligand (PLP), 5 pockets (best druggability 0.73). MolNFT v1 #118694 on…
- PDB
- 5F9S
- 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
- PLP
- Pockets
- 5 · best druggability 0.73
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
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.73 | 0.96 | 27 | PLP |
| 2 | 284 | 0.61 | 0.79 | 36 | empty |
| 3 | 272 | 0.53 | 0.75 | 28 | empty |
| 4 | 55 | 0.39 | 0.80 | 14 | empty |
| 5 | 87 | 0.32 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4061 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5F9S · Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at… · 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 5F9S · PDBe 5F9S · UniProt P21549
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