MolNFT v1 · #167408 · protein
Crystal structure of cystathionine beta synthase from legionella pneumophila with llp, plp, and homocysteine
6VJU · Cystathionine beta-lyase: “Crystal structure of cystathionine beta synthase from legionella pneumophila with llp, plp, and homocysteine”. X-ray diffraction, 2 ligands (HCS, PLP), 7 pockets (best druggability 0.77). MolNFT v1 #167408…
- 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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