Research workbench
Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine
Analyse Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DYT
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine phenol-lyase
- EC
- 4.1.99.2
- UniProt
- P31013
- Ligands
- F0G, PP3, K
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 44% helix, 15% strand | P31013 |
Ligands and binding sites
- F0G · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine · ligand · chains A, B
- PP3 · Alanyl-pyridoxal-5'-phosphate · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.96 | 41 | F0G |
| 2 | 752 | 0.79 | 0.83 | 74 | PP3 |
| 3 | 524 | 0.72 | 0.81 | 46 | empty |
| 4 | 571 | 0.72 | 0.80 | 45 | empty |
| 5 | 233 | 0.61 | 0.81 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2432 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6DYT · Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine · the same entry in another collection · chain B against B, TM-score 1.00
- P31013 · AlphaFold monomer V2.0 prediction for tyrosine phenol-lyase (P31013) · a predicted model of the same protein · chain A 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 P31013
- Elsewhere: RCSB PDB 6DYT · PDBe 6DYT · UniProt P31013
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