Research workbench
Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex complexed with plp-glycine
Analyse Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UXI
- Type
- protein
- Length
- 925 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- K4FZF8
- Ligands
- PLG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 462 | 48% helix, 14% strand | K4FZF8 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 463 | 48% helix, 14% strand | K4FZF8 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 21 | empty |
| 2 | 347 | 0.72 | 0.84 | 41 | PLG |
| 3 | 333 | 0.71 | 0.84 | 46 | PLG |
| 4 | 407 | 0.64 | 0.78 | 42 | EDO |
| 5 | 52 | 0.43 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4849 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 6UXI · Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed… · 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 K4FZF8
- Elsewhere: RCSB PDB 6UXI · PDBe 6UXI · UniProt K4FZF8
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