MolNFT v1 · #170161 · protein
Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma gondii with L-serine
6XYL: “Crystal structure of DELTA466-491 cystathionine beta-synthase from toxoplasma gondii with L-serine”. X-ray diffraction, 1 ligand (P1T), 20 pockets (best druggability 0.83). MolNFT v1 #170161 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XYL
- Type
- protein
- Length
- 2,833 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
- P1T
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 468 | 41% helix, 16% strand | A0A125YSJ9 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 469 | 41% helix, 17% strand | A0A125YSJ9 |
| C | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 470 | 40% helix, 17% strand | A0A125YSJ9 |
| D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 42% helix, 17% strand | A0A125YSJ9 |
| E | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 476 | 40% helix, 17% strand | A0A125YSJ9 |
| F | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 475 | 40% 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 · 6 copies · chains A, B, C, D, E, F
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 | 718 | 0.83 | 0.86 | 71 | empty |
| 2 | 197 | 0.80 | 0.94 | 31 | empty |
| 3 | 164 | 0.79 | 0.95 | 31 | empty |
| 4 | 99 | 0.78 | 0.99 | 30 | P1T |
| 5 | 245 | 0.78 | 0.91 | 39 | empty |
Interfaces
9 interfaces between chains.
- C–E · 4549 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 4485 Ų buried · 45 hydrogen bonds · protein-protein
- A–F · 4462 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 285 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6XYL · Crystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with… · the same entry in another collection · chain C against C, 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 6XYL · PDBe 6XYL · UniProt A0A125YSJ9
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