Research workbench
Crystal structure of cystathionine beta synthase from legionella pneumophila with llp, plp, and homocysteine
Analyse Crystal structure of cystathionine beta synthase from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJU
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase
- UniProt
- A0A2S6F0T8
- Ligands
- HCS, PLP
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cystathionine beta-lyase | protein | 317 | 40% helix, 18% strand | A0A2S6F0T8 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.77 | 0.98 | 20 | ACT |
| 2 | 81 | 0.74 | 0.98 | 28 | ACT, PLP |
| 3 | 180 | 0.74 | 0.91 | 31 | EDO |
| 4 | 234 | 0.70 | 0.86 | 33 | empty |
| 5 | 267 | 0.55 | 0.77 | 35 | EDO, ACT |
Interfaces
1 interface between chains.
- A–B · 1957 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6VJU · Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP… · the same entry in another collection · chain B against B, 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 A0A2S6F0T8
- Elsewhere: RCSB PDB 6VJU · PDBe 6VJU · UniProt A0A2S6F0T8
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