Research workbench
Manipulating the regioselectivity of phenylalanine aminomutase: new insights into the reaction mechanism of mio-dependent enzymes from structure-guided directed evolution
Analyse Manipulating the regioselectivity of phenylalanine aminomutase: new insights… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YII
- Type
- protein
- Length
- 2,585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine ammonia-lyase
- EC
- 5.4.3.-, 4.3.1.24
- UniProt
- Q68G84
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine ammonia-lyase (EC 5.4.3.-, 4.3.1.24) | protein | 644 | 64% helix, 5% strand | Q68G84 |
| B | Phenylalanine ammonia-lyase (EC 5.4.3.-, 4.3.1.24) | protein | 650 | 63% helix, 5% strand | Q68G84 |
| C | Phenylalanine ammonia-lyase (EC 5.4.3.-, 4.3.1.24) | protein | 646 | 63% helix, 5% strand | Q68G84 |
| D | Phenylalanine ammonia-lyase (EC 5.4.3.-, 4.3.1.24) | protein | 645 | 64% helix, 5% strand | Q68G84 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, C, B, D
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.83 | 0.84 | 129 | BME |
| 2 | 1130 | 0.81 | 0.82 | 114 | BME |
| 3 | 75 | 0.74 | 0.98 | 30 | empty |
| 4 | 62 | 0.74 | 0.99 | 25 | empty |
| 5 | 806 | 0.73 | 0.78 | 75 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4044 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 4031 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 3936 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 3926 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 1277 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 modified (additive adduct, nonstandard).
Compared structures
- 2YII · Manipulating the regioselectivity of phenylalanine aminomutase: new insights into the… · the same entry in another collection · chain B against B, TM-score 1.00
- Q68G84 · AlphaFold monomer V2.0 prediction for phenylalanine aminomutase (L-beta-phenylalanine… · a predicted model of the same protein · 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 Q68G84
- Elsewhere: RCSB PDB 2YII · PDBe 2YII · UniProt Q68G84
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