Research workbench
Crystal structure of Y60ABSSHMT crystallized in the presence of glycine
Analyse Crystal structure of Y60ABSSHMT crystallized in the presence of glycine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VMS
- Type
- protein
- Length
- 405 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q7SIB6
- Ligands
- GLY, PLP, PO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 405 | 51% helix, 14% strand | Q7SIB6 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.40 | 0.76 | 16 | empty |
| 2 | 146 | 0.40 | 0.74 | 21 | GLY |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2VMS · Crystal structure of Y60AbsSHMT crystallized in the presence of Glycine · the same entry in another collection · 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 Q7SIB6
- Elsewhere: RCSB PDB 2VMS · PDBe 2VMS · UniProt Q7SIB6
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