Research workbench
Crystal structure of serine hydroxymethyltransferase complexed with glycine and 5-formyl tetrahydrofolate
Analyse Crystal structure of serine hydroxymethyltransferase complexed with glycine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KL2
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q7SIB6
- Ligands
- PLP, GLY, FON
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 405 | 50% helix, 14% strand | Q7SIB6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains A, B
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.77 | 0.87 | 59 | PLP, GLY, FON |
| 2 | 346 | 0.75 | 0.86 | 61 | PLP, GLY, FON |
| 3 | 102 | 0.70 | 0.92 | 19 | empty |
| 4 | 260 | 0.52 | 0.75 | 24 | empty |
| 5 | 133 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4000 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 1KL2 · Crystal Structure of Serine Hydroxymethyltransferase Complexed with Glycine and 5-formyl… · 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 1KL2 · PDBe 1KL2 · UniProt Q7SIB6
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