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Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma gondii with L-cystathionine
Analyse Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y21
- Type
- protein
- Length
- 1,425 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- A0A125YSJ9
- Ligands
- P1T
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 42% helix, 17% strand | A0A125YSJ9 |
Ligands and binding sites
- P1T · 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]acrylic acid · ligand · 3 copies · chains D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.77 | 0.97 | 30 | P1T |
| 2 | 254 | 0.77 | 0.90 | 39 | empty |
| 3 | 91 | 0.76 | 0.98 | 27 | P1T |
| 4 | 278 | 0.76 | 0.89 | 40 | empty |
| 5 | 101 | 0.76 | 0.97 | 27 | P1T |
Interfaces
2 interfaces between chains.
- A–B · 4527 Ų buried · 46 hydrogen bonds · protein-protein
- D–A · 239 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y21 · Crystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with… · 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 A0A125YSJ9
- Elsewhere: RCSB PDB 6Y21 · PDBe 6Y21 · UniProt A0A125YSJ9
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