MolNFT v1 · #166680 · protein
Structure of serine hydroxymethyltransferase 8 from glycine max cultivar forrest complexed with plp-glycine
6UXL: “Structure of serine hydroxymethyltransferase 8 from glycine max cultivar forrest complexed with plp-glycine”. X-ray diffraction, 1 ligand (PLG), 9 pockets (best druggability 0.75). MolNFT v1 #166680 on GenesisL1: 3D structure…
- PDB
- 6UXL
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- K4FW35
- Ligands
- PLG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 461 | 47% helix, 14% strand | K4FW35 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.98 | 16 | empty |
| 2 | 346 | 0.70 | 0.83 | 45 | PLG |
| 3 | 312 | 0.69 | 0.83 | 47 | PLG |
| 4 | 312 | 0.59 | 0.77 | 38 | empty |
| 5 | 50 | 0.44 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4939 Ų buried · 62 hydrogen bonds · protein-protein
Compared structures
- 6UXL · Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Forrest… · 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 K4FW35
- Elsewhere: RCSB PDB 6UXL · PDBe 6UXL · UniProt K4FW35
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