Research workbench
Phenylalanine ammonia-lyase (pal) from petroselinum crispum complexed with S-appa
Analyse Phenylalanine ammonia-lyase (pal) from petroselinum crispum complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F6T
- Type
- protein
- Length
- 1,352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine ammonia-lyase 1
- EC
- 4.3.1.24
- UniProt
- P24481
- Ligands
- CV2
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine ammonia-lyase 1 (EC 4.3.1.24) | protein | 675 | 61% helix, 4% strand | P24481 |
| B | Phenylalanine ammonia-lyase 1 (EC 4.3.1.24) | protein | 677 | 60% helix, 4% strand | P24481 |
Ligands and binding sites
- CV2 · (S)-(1-amino-2phenylallyl)phosphonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.82 | 0.82 | 94 | empty |
| 2 | 102 | 0.57 | 0.85 | 22 | CV2 |
| 3 | 141 | 0.57 | 0.83 | 31 | empty |
| 4 | 114 | 0.56 | 0.84 | 28 | empty |
| 5 | 98 | 0.55 | 0.84 | 24 | CV2 |
Interfaces
1 interface between chains.
- A–B · 4117 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 6F6T · Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum complexed with S-APPA · the same entry in another collection · chain B against B, TM-score 1.00
- P24481 · AlphaFold monomer V2.0 prediction for phenylalanine ammonia-lyase 1 (P24481) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P24481
- Elsewhere: RCSB PDB 6F6T · PDBe 6F6T · UniProt P24481
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