MolNFT v1 · #144724 · protein
Crystal structures of cystathionine beta-synthase from saccharomyces cerevisiae: the structure of the catalytic core
6C2H: “Crystal structures of cystathionine beta-synthase from saccharomyces cerevisiae: the structure of the…”. X-ray diffraction, 4 ligands (PLP, CA, NA), 3 pockets (best druggability 0.73). MolNFT v1 #144724 on GenesisL1: 3D structure…
- PDB
- 6C2H
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- P32582
- Ligands
- PLP, CA, NA, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 345 | 42% helix, 17% strand | P32582 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.98 | 28 | PLP, ACT |
| 2 | 167 | 0.65 | 0.86 | 27 | CL |
| 3 | 83 | 0.34 | 0.75 | 14 | PGE |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6C2H · Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the… · the same entry in another collection · chain A against A, TM-score 1.00
- P32582 · AlphaFold monomer V2.0 prediction for cystathionine beta-synthase (P32582) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P32582
- Elsewhere: RCSB PDB 6C2H · PDBe 6C2H · UniProt P32582
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