Research workbench
Crystal structures of cystathionine beta-synthase from saccharomyces cerevisiae: the structure of the pmp complex
Analyse Crystal structures of cystathionine beta-synthase from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C4P
- Type
- protein
- Length
- 344 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
- PMP, CA, NA, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 344 | 40% helix, 17% strand | P32582 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.78 | 0.90 | 49 | PMP, CL |
| 2 | 84 | 0.34 | 0.74 | 13 | PEG |
Compared structures
- 6C4P · 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 6C4P · PDBe 6C4P · UniProt P32582
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