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
- 6DZ5
- Type
- protein
- Length
- 907 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
- P61, K
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 452 | 44% helix, 13% strand | P31013 |
| B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 43% helix, 15% strand | P31013 |
Ligands and binding sites
- P61 · (2E)-3-(3-fluoro-4-hydroxyphenyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid · ligand · 2 copies · 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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.81 | 0.84 | 75 | P61 |
| 2 | 565 | 0.78 | 0.85 | 71 | P61 |
| 3 | 533 | 0.72 | 0.81 | 45 | empty |
| 4 | 529 | 0.72 | 0.81 | 47 | empty |
| 5 | 245 | 0.62 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2322 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6DZ5 · Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine · the same entry in another collection · chain A against A, 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 0.97
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 P31013
- Elsewhere: RCSB PDB 6DZ5 · PDBe 6DZ5 · UniProt P31013
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