MolNFT v1 · #156481 · protein
Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with pyridoxal 5'-phosphate (plp) and glycodeoxycholic acid
6M5O · Serine hydroxymethyltransferase, mitochondrial: “Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with pyridoxal 5'-phosphate (plp)…”. X-ray diffraction, 2 ligands (DXC, GLY), 15 pockets (best druggability…
- PDB
- 6M5O
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, mitochondrial
- EC
- 2.1.2.1
- UniProt
- P34897
- Ligands
- DXC, GLY
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 462 | 49% helix, 15% strand | P34897 |
Ligands and binding sites
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 24 | empty |
| 2 | 450 | 0.74 | 0.83 | 42 | DXC, GLY |
| 3 | 428 | 0.73 | 0.83 | 38 | DXC, GLY |
| 4 | 63 | 0.42 | 0.82 | 15 | empty |
| 5 | 114 | 0.39 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4634 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6M5O · Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal… · the same entry in another collection · chain A against A, TM-score 1.00
- P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · 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 P34897
- Elsewhere: RCSB PDB 6M5O · PDBe 6M5O · UniProt P34897
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