MolNFT v1 · #5487 · protein
Recombinant serine hydroxymethyltransferase (mouse)
1EJI: “Recombinant serine hydroxymethyltransferase (mouse)”. X-ray diffraction, 2 ligands (PLG, THF), 20 pockets (best druggability 0.81). MolNFT v1 #5487 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EJI
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- P50431
- Ligands
- PLG, THF
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 478 | 48% helix, 13% strand | P50431 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 4 copies · chains A, B, C, D
- THF · 5-hydroxymethylene-6-hydrofolic acid · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.81 | 0.97 | 44 | empty |
| 2 | 106 | 0.80 | 0.98 | 23 | empty |
| 3 | 323 | 0.79 | 0.89 | 45 | PLG, THF |
| 4 | 770 | 0.76 | 0.81 | 94 | PLG, THF |
| 5 | 457 | 0.76 | 0.85 | 69 | PLG, THF |
Interfaces
6 interfaces between chains.
- A–B · 5144 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4971 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 823 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 810 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 1EJI · Recombinant serine hydroxymethyltransferase (mouse) · the same entry in another collection · chain D against D, TM-score 1.00
- P50431 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P50431) · a predicted model of the same protein · chain B 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 P50431
- Elsewhere: RCSB PDB 1EJI · PDBe 1EJI · UniProt P50431
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