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Crystal structure of phenylalanine ammonia-lyase from yeast rhododporidium toruloides
Analyse Crystal structure of phenylalanine ammonia-lyase from yeast rhododporidium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y2M
- Type
- protein
- Length
- 2,659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine ammonia-lyase
- EC
- 4.3.1.5
- UniProt
- P11544
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine ammonia-lyase (EC 4.3.1.5) | protein | 665 | 61% helix, 6% strand | P11544 |
| B | Phenylalanine ammonia-lyase (EC 4.3.1.5) | protein | 669 | 61% helix, 5% strand | P11544 |
| C | Phenylalanine ammonia-lyase (EC 4.3.1.5) | protein | 664 | 61% helix, 5% strand | P11544 |
| D | Phenylalanine ammonia-lyase (EC 4.3.1.5) | protein | 661 | 61% helix, 6% strand | P11544 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.84 | 0.88 | 94 | empty |
| 2 | 728 | 0.84 | 0.88 | 95 | empty |
| 3 | 162 | 0.83 | 0.99 | 38 | empty |
| 4 | 174 | 0.83 | 0.98 | 38 | empty |
| 5 | 969 | 0.83 | 0.84 | 95 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4442 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 4433 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3361 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 3354 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 1458 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified (engineered).
Compared structures
- 1Y2M · Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides · the same entry in another collection · chain D against D, TM-score 1.00
- P11544 · AlphaFold monomer V2.0 prediction for PHENYLALANINE/TYROSINE ammonia- lyase (P11544) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P11544
- Elsewhere: RCSB PDB 1Y2M · PDBe 1Y2M · UniProt P11544
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