Research workbench
Crystal structure of L-serine hydroxymethyltransferase in complex with a mixture of L-threonine and glycine
Analyse Crystal structure of L-serine hydroxymethyltransferase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WXG
- 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
- 2BO, NA
- Pockets
- 8 · best druggability 0.76
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
- 2BO · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 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 | 396 | 0.76 | 0.86 | 48 | 2BO |
| 2 | 394 | 0.75 | 0.85 | 48 | 2BO |
| 3 | 224 | 0.67 | 0.84 | 24 | empty |
| 4 | 135 | 0.38 | 0.73 | 23 | empty |
| 5 | 70 | 0.36 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 3487 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 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 4WXG · PDBe 4WXG · UniProt Q5M0B4
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