MolNFT v1 · #171407 · protein
Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma gondii with O-acetylserine
6Z3S: “Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma gondii with O-acetylserine”. X-ray diffraction, 1 ligand (P1T), 19 pockets (best druggability 0.79). MolNFT v1 #171407 on GenesisL1: 3D structure, binding…
- PDB
- 6Z3S
- Type
- protein
- Length
- 1,405 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
- 19 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 468 | 41% helix, 16% strand | A0A125YSJ9 |
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 41% helix, 17% strand | A0A125YSJ9 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 462 | 43% helix, 16% 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
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.79 | 0.91 | 36 | empty |
| 2 | 266 | 0.78 | 0.91 | 37 | empty |
| 3 | 96 | 0.78 | 0.98 | 27 | P1T |
| 4 | 82 | 0.75 | 0.98 | 26 | P1T |
| 5 | 82 | 0.75 | 0.98 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4485 Ų buried · 41 hydrogen bonds · protein-protein
- D–A · 280 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6Z3S · Crystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with… · the same entry in another collection · chain D against D, 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 6Z3S · PDBe 6Z3S · UniProt A0A125YSJ9
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