Research workbench

D214A mutant of tyrosine phenol-lyase from citrobacter freundii

Analyse D214A mutant of tyrosine phenol-lyase from citrobacter freundii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YHK
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: PLP, K
Pockets: 10 · best druggability 0.79

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	455	45% helix, 15% strand	P31013

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 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

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	789	0.79	0.83	85	PLP
2	696	0.78	0.83	74	PEG, PLP
3	529	0.71	0.80	48	empty
4	487	0.70	0.80	47	empty
5	188	0.50	0.77	26	empty

Interfaces

1 interface between chains.

A–B · 2603 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

2YHK · D214A mutant of tyrosine phenol-lyase from Citrobacter freundii · 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 0.96

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 2YHK · PDBe 2YHK · UniProt P31013

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