Research workbench
Crystal structure of beta-cyanoalanine synthase in soybean
Analyse Crystal structure of beta-cyanoalanine synthase in soybean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VBE
- Type
- protein
- Length
- 1,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-cyanoalnine synthase
- EC
- 2.5.1.47
- Ligands
- PLP
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 317 | 44% helix, 18% strand | — |
| B | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 321 | 43% helix, 18% strand | — |
| C | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 329 | 42% helix, 17% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.72 | 0.80 | 75 | PLP |
| 2 | 560 | 0.71 | 0.80 | 64 | PLP |
| 3 | 66 | 0.69 | 0.96 | 28 | PLP |
| 4 | 67 | 0.69 | 0.95 | 25 | PLP |
| 5 | 475 | 0.66 | 0.78 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2974 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2850 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 665 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3VBE · Crystal structure of beta-cyanoalanine synthase in soybean · 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
- Elsewhere: RCSB PDB 3VBE · PDBe 3VBE
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