MolNFT v1 · #109260 · protein
Crystal structure of L-serine hydroxymethyltransferase in complex with glycine
4WXF: “Crystal structure of L-serine hydroxymethyltransferase in complex with glycine”. X-ray diffraction, 1 ligand (PLG), 8 pockets (best druggability 0.77). MolNFT v1 #109260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WXF
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q5M0B4
- Ligands
- PLG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 410 | 49% helix, 13% strand | Q5M0B4 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.77 | 0.88 | 44 | PLG |
| 2 | 365 | 0.74 | 0.85 | 50 | PLG |
| 3 | 244 | 0.69 | 0.84 | 25 | empty |
| 4 | 158 | 0.43 | 0.74 | 21 | empty |
| 5 | 73 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 3470 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 4WXF · Crystal structure of L-Serine Hydroxymethyltransferase in complex with glycine · the same entry in another collection · chain C against C, TM-score 1.00
- Q5M0B4 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (Q5M0B4) · 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 Q5M0B4
- Elsewhere: RCSB PDB 4WXF · PDBe 4WXF · UniProt Q5M0B4
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