Research workbench
Cystathionine beta-synthase from toxoplasma gondii
Analyse Cystathionine beta-synthase from toxoplasma gondii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XWL
- Type
- protein
- Length
- 2,841 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- A0A125YSJ9
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 474 | 41% helix, 16% strand | A0A125YSJ9 |
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 471 | 43% helix, 17% strand | A0A125YSJ9 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 469 | 42% helix, 17% strand | A0A125YSJ9 |
| C | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 477 | 41% helix, 17% strand | A0A125YSJ9 |
| D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 41% helix, 17% strand | A0A125YSJ9 |
| E | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 41% helix, 17% strand | A0A125YSJ9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains F, A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.84 | 0.87 | 72 | empty |
| 2 | 111 | 0.79 | 0.98 | 21 | empty |
| 3 | 187 | 0.78 | 0.93 | 37 | empty |
| 4 | 234 | 0.78 | 0.91 | 37 | empty |
| 5 | 105 | 0.77 | 0.97 | 19 | empty |
Interfaces
9 interfaces between chains.
- C–E · 4585 Ų buried · 47 hydrogen bonds · protein-protein
- F–A · 4531 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 4492 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 714 Ų buried · 8 hydrogen bonds · protein-protein
- F–D · 203 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6XWL · Cystathionine beta-synthase from Toxoplasma gondii · the same entry in another collection · chain E against E, 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 A0A125YSJ9
- Elsewhere: RCSB PDB 6XWL · PDBe 6XWL · UniProt A0A125YSJ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.