Research workbench
Crystal structure of serine hydroxymethyltransferase with covalently bound plp schiff-base from plasmodium falciparum
Analyse Crystal structure of serine hydroxymethyltransferase with covalently bound plp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O6Z
- Type
- protein
- Length
- 1,779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q8I566
- Ligands
- PLP, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 448 | 48% helix, 14% strand | Q8I566 |
| B, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 445 | 50% helix, 12% strand | Q8I566 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 441 | 49% helix, 14% strand | Q8I566 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.82 | 0.88 | 89 | PLP, PO4 |
| 2 | 503 | 0.80 | 0.86 | 74 | PLP |
| 3 | 308 | 0.72 | 0.85 | 26 | empty |
| 4 | 551 | 0.71 | 0.80 | 61 | empty |
| 5 | 351 | 0.57 | 0.75 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4878 Ų buried · 81 hydrogen bonds · protein-protein
- C–D · 4553 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 756 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 4O6Z · Crystal structure of serine hydroxymethyltransferase with covalently bound PLP… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I566 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (Q8I566) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8I566
- Elsewhere: RCSB PDB 4O6Z · PDBe 4O6Z · UniProt Q8I566
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.