MolNFT v1 · #55188 · protein
Y71F mutant of tyrosine phenol-lyase from citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine
2YCN: “Y71F mutant of tyrosine phenol-lyase from citrobacter freundii in complex with quinonoid intermediate formed…”. X-ray diffraction, 2 ligands (P61, K), 12 pockets (best druggability 0.82). MolNFT v1 #55188 on GenesisL1: 3D structure…
- PDB
- 2YCN
- Type
- protein
- Length
- 912 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
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 456 | 45% 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
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.82 | 0.98 | 41 | P61 |
| 2 | 784 | 0.78 | 0.82 | 84 | P61 |
| 3 | 503 | 0.72 | 0.81 | 46 | empty |
| 4 | 517 | 0.71 | 0.80 | 45 | empty |
| 5 | 247 | 0.61 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2323 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2YCN · Y71F mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid… · 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 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 P31013
- Elsewhere: RCSB PDB 2YCN · PDBe 2YCN · UniProt P31013
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