Research workbench
Structural characterization of beta cyanoalanine synthase from tetranychus urticae
Analyse Structural characterization of beta cyanoalanine synthase from tetranychus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PMU
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-cyanoalanine synthase
- UniProt
- T1KF23
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-cyanoalanine synthase | protein | 279 | 44% helix, 20% strand | T1KF23 |
| B | Beta-cyanoalanine synthase | protein | 284 | 45% helix, 19% strand | T1KF23 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.75 | 0.80 | 110 | PLP |
| 2 | 72 | 0.72 | 0.97 | 19 | empty |
| 3 | 100 | 0.39 | 0.76 | 20 | empty |
| 4 | 86 | 0.36 | 0.76 | 19 | empty |
| 5 | 78 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1999 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6PMU · Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae · 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 T1KF23
- Elsewhere: RCSB PDB 6PMU · PDBe 6PMU · UniProt T1KF23
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