Research workbench
Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex complexed with plp
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
- 6UXH
- Type
- protein
- Length
- 923 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
- Pockets
- 9 · best druggability 0.78
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 | 461 | 49% helix, 14% strand | K4FZF8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 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 | 94 | 0.78 | 0.98 | 23 | empty |
| 2 | 403 | 0.70 | 0.81 | 38 | empty |
| 3 | 370 | 0.69 | 0.82 | 35 | empty |
| 4 | 365 | 0.63 | 0.78 | 39 | EDO |
| 5 | 55 | 0.45 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4790 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6UXH · 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 6UXH · PDBe 6UXH · UniProt K4FZF8
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