Research workbench
Crystal structure of beta-cyanoalanine synthase K95A mutant in soybean
Analyse Crystal structure of beta-cyanoalanine synthase K95A mutant in soybean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VC3
- Type
- protein
- Length
- 1,934 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-cyanoalnine synthase
- EC
- 2.5.1.47
- Ligands
- C6P
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 322 | 45% helix, 18% strand | — |
| D | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 323 | 44% helix, 18% strand | — |
| F | Beta-cyanoalnine synthase (EC 2.5.1.47) | protein | 323 | 44% helix, 17% strand | — |
Ligands and binding sites
- C6P · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-cysteine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.82 | 0.98 | 31 | C6P |
| 2 | 136 | 0.81 | 0.98 | 32 | C6P |
| 3 | 137 | 0.81 | 0.98 | 32 | C6P |
| 4 | 140 | 0.81 | 0.98 | 32 | C6P |
| 5 | 138 | 0.81 | 0.98 | 31 | C6P |
Interfaces
9 interfaces between chains.
- C–D · 3316 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3244 Ų buried · 35 hydrogen bonds · protein-protein
- C–E · 561 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3VC3 · Crystal structure of beta-cyanoalanine synthase K95A mutant 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 3VC3 · PDBe 3VC3
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