Research workbench
Crystal structure of cystathionine beta-synthase from lactobacillus plantarum
Analyse Crystal structure of cystathionine beta-synthase from lactobacillus plantarum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B1H
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- F9UT54
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 303 | 44% helix, 19% strand | F9UT54 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.78 | 0.96 | 30 | empty |
| 2 | 452 | 0.69 | 0.80 | 41 | SO4 |
| 3 | 299 | 0.69 | 0.83 | 34 | SO4 |
| 4 | 345 | 0.69 | 0.82 | 39 | SO4 |
| 5 | 368 | 0.66 | 0.80 | 42 | SO4 |
Interfaces
1 interface between chains.
- A–C · 1724 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5B1H · Crystal structure of cystathionine beta-synthase from Lactobacillus plantarum · the same entry in another collection · chain A against A, 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 F9UT54
- Elsewhere: RCSB PDB 5B1H · PDBe 5B1H · UniProt F9UT54
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