MolNFT v1 · #20972 · protein
E75Q mutant of rabbit cytosolic serine hydroxymethyltransferase, complex with glycine
1RVY · Serine hydroxymethyltransferase, cytosolic: “E75Q mutant of rabbit cytosolic serine hydroxymethyltransferase, complex with glycine”. X-ray diffraction, 3 ligands (PLG, PLP, PO4), 11 pockets (best druggability 0.77). MolNFT v1 #20972…
- PDB
- 1RVY
- Type
- protein
- Length
- 929 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, cytosolic
- EC
- 2.1.2.1
- UniProt
- P07511
- Ligands
- PLG, PLP, PO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 463 | 51% helix, 14% strand | P07511 |
| B | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 466 | 49% helix, 14% strand | P07511 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 23 | empty |
| 2 | 368 | 0.74 | 0.85 | 41 | PLG |
| 3 | 397 | 0.73 | 0.84 | 58 | PO4, PLP |
| 4 | 52 | 0.70 | 0.98 | 26 | empty |
| 5 | 212 | 0.52 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 4621 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 1RVY · E75Q mutant of rabbit cytosolic serine hydroxymethyltransferase, complex with glycine · the same entry in another collection · chain B against B, TM-score 1.00
- P07511 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P07511) · 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 P07511
- Elsewhere: RCSB PDB 1RVY · PDBe 1RVY · UniProt P07511
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