MolNFT v1 · #126156 · protein
Crystal structure of the D183N variant of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) at 1.8 ångström; internal aldimine with plp in the active site
5LUC · Serine--pyruvate aminotransferase: “Crystal structure of the D183N variant of human ALANINE:GLYOXYLATE aminotransferase major allele (agt-ma) at…”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5LUC
- Type
- protein
- Length
- 3,090 residues
- Chains
- 8
- 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
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 387 | 42% helix, 15% strand | P21549 |
| B, E, G, M, S, T | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 386 | 42% helix, 15% strand | P21549 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, E, G, M, N, S, T
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 8 copies · chains A, B, E, G, M, N, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.77 | 0.81 | 66 | empty |
| 2 | 799 | 0.74 | 0.79 | 70 | empty |
| 3 | 832 | 0.74 | 0.78 | 71 | empty |
| 4 | 314 | 0.69 | 0.83 | 46 | PLP |
| 5 | 307 | 0.69 | 0.83 | 48 | PLP |
Interfaces
11 interfaces between chains.
- A–B · 4145 Ų buried · 48 hydrogen bonds · protein-protein
- M–N · 4136 Ų buried · 48 hydrogen bonds · protein-protein
- S–T · 4125 Ų buried · 46 hydrogen bonds · protein-protein
- E–G · 4088 Ų buried · 47 hydrogen bonds · protein-protein
- A–N · 542 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LUC · Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major… · the same entry in another collection · chain T against T, 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 5LUC · PDBe 5LUC · UniProt P21549
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.