Research workbench
Serine hydroxymethyltransferase from salmonella typhimurium
Analyse Serine hydroxymethyltransferase from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBX
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- P0A2E1
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 390 | 49% helix, 14% strand | P0A2E1 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 383 | 48% helix, 14% strand | P0A2E1 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.68 | 0.78 | 61 | empty |
| 2 | 431 | 0.63 | 0.77 | 44 | empty |
| 3 | 296 | 0.52 | 0.74 | 33 | empty |
| 4 | 214 | 0.51 | 0.76 | 23 | empty |
| 5 | 121 | 0.48 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3700 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3GBX · Serine hydroxymethyltransferase from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
- P0A2E1 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (P0A2E1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0A2E1
- Elsewhere: RCSB PDB 3GBX · PDBe 3GBX · UniProt P0A2E1
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