MolNFT v1 · #178544 · protein

Tyrosine phenol-lyase from pantoea agglomerans

7FJK: “Tyrosine phenol-lyase from pantoea agglomerans”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.76). MolNFT v1 #178544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7FJK
Type: protein
Length: 1,824 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine phenol-lyase
EC: 4.1.99.2
UniProt: P31011
Ligands: PLP
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tyrosine phenol-lyase (EC 4.1.99.2)	protein	456	46% helix, 17% strand	P31011

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 59 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · chains A, B, C, D
CIT · Citric acid · additive · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	652	0.76	0.82	76	PLP
2	676	0.76	0.81	77	PLP, EDO, CIT
3	659	0.75	0.81	72	PLP
4	81	0.75	0.98	29	PLP
5	610	0.72	0.79	57	EDO

Interfaces

6 interfaces between chains.

B–D · 2446 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 2445 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1789 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1779 Å² buried · 39 hydrogen bonds · protein-protein
B–C · 388 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).

Compared structures

7FJK · Tyrosine phenol-lyase from pantoea agglomerans · the same entry in another collection · chain A against A, TM-score 1.00
P31011 · AlphaFold monomer V2.0 prediction for tyrosine phenol-lyase (P31011) · 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 P31011
Elsewhere: RCSB PDB 7FJK · PDBe 7FJK · UniProt P31011

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