MolNFT v1 · #156489 · protein
Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with pyridoxal 5'-phosphate (plp) and glycodeoxycholic acid
6M5W · Serine hydroxymethyltransferase, cytosolic: “Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with pyridoxal 5'-phosphate (plp)…”. X-ray diffraction, 3 ligands (PLP, DXC, GLY), 3 pockets (best druggability…
- PDB
- 6M5W
- Type
- protein
- Length
- 470 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, cytosolic
- EC
- 2.1.2.1
- UniProt
- P34896
- Ligands
- PLP, DXC, GLY
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 470 | 49% helix, 14% strand | P34896 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · chains A
- GLY · Glycine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.48 | 0.75 | 24 | empty |
| 2 | 54 | 0.40 | 0.82 | 19 | PLP |
| 3 | 74 | 0.28 | 0.72 | 18 | empty |
Compared structures
- 6M5W · Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal… · the same entry in another collection · chain A against A, TM-score 1.00
- P34896 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P34896) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P34896
- Elsewhere: RCSB PDB 6M5W · PDBe 6M5W · UniProt P34896
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.