Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Jan 2021.
Explore 6M5W in 3D Show helices and sheets RCSB PDB PDBe
6M5W contains 25 α-helices and 24 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 15-23 | 9 | |
| α-helix | 26-29 | 4 | |
| α-helix | 31-45 | 15 | |
| β-strand | 48-49 | 2 | 1 |
| β-strand | 51 | 1 | 2 |
| α-helix | 59-65 | 7 | |
| α-helix | 68-70 | 3 | |
| β-strand | 76-77 | 2 | 3 |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 88-103 | 16 | |
| β-strand | 111-114 | 4 | 4 |
| α-helix | 120-131 | 12 | |
| β-strand | 137-139 | 3 | 4 |
| β-strand | 141 | 1 | 5 |
| α-helix | 149-151 | 3 | |
| β-strand | 154 | 1 | 6 |
| β-strand | 159 | 1 | 6 |
| α-helix | 162-166 | 5 | |
| β-strand | 168-169 | 2 | 4 |
| β-strand | 172 | 1 | 5 |
| β-strand | 174 | 1 | 7 |
| β-strand | 181 | 1 | 7 |
| α-helix | 183-193 | 11 | |
| β-strand | 197-201 | 5 | 4 |
| α-helix | 211-221 | 11 | |
| β-strand | 224-228 | 5 | 4 |
| α-helix | 229-231 | 3 | |
| α-helix | 233-238 | 6 | |
| α-helix | 244-246 | 3 | |
| β-strand | 250-254 | 5 | 4 |
| α-helix | 257-259 | 3 | |
| β-strand | 265-270 | 6 | 4 |
| β-strand | 272-273 | 2 | 8 |
| β-strand | 285-286 | 2 | 8 |
| α-helix | 288-294 | 7 | |
| α-helix | 295-300 | 6 | |
| α-helix | 306-319 | 14 | |
| α-helix | 322-344 | 23 | |
| β-strand | 348-349 | 2 | 2 |
| β-strand | 358-362 | 5 | 2 |
| α-helix | 363-365 | 3 | |
| α-helix | 370-379 | 10 | |
| β-strand | 382-383 | 2 | 1 |
| β-strand | 385-387 | 3 | 2 |
| β-strand | 400-404 | 5 | 2 |
| α-helix | 406-409 | 4 | |
| α-helix | 415-439 | 25 | |
| α-helix | 445-453 | 9 | |
| α-helix | 455-472 | 18 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Serine hydroxymethyltransferase, cytosolic | A | protein | 503 | Homo sapiens | P34896 (AlphaFold model) |
>6M5W_1 Serine hydroxymethyltransferase, cytosolic (chains A) MGSSHHHHHHSSGLVPRGSHMTMPVNGAHKDADLWSSHDKMLAQPLKDSDVEVYNIIKKE SNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRA LQAYKLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKI SATSIFFESMPYKVNPDTGYINYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADE NGAYLMADMAHISGLVAAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKT GKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSE ALTELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSG LRLGTPALTSRGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAA VQALREEVESFASLFPLPGLPDF
| ID | Name | Formula | Copies |
|---|---|---|---|
| GLY | Glycine | C2 H5 N O2 | 1 |
| DXC | (3ALPHA,5BETA,12ALPHA)-3,12-dihydroxycholan-24-oic acid | C24 H40 O4 | 1 |
| PLP | Pyridoxal-5'-phosphate | C8 H10 N O6 P | 1 |
Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate. Ota, T., Senoo, A., Shirakawa, M. et al. iScience (2021) 24:102036-102036. DOI 10.1016/j.isci.2021.102036 · PubMed
Other PDB entries of the same protein (UniProt P34896 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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