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Crystal structure of vioe complexed with phenylpyruvic acid

Analyse Crystal structure of vioe complexed with phenylpyruvic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZF4
Type: protein
Length: 1,087 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein vioe
UniProt: Q7NSZ5
Ligands: PPY
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein vioe	protein	187	6% helix, 55% strand	Q7NSZ5
B	Hypothetical protein vioe	protein	180	7% helix, 55% strand	Q7NSZ5
C	Hypothetical protein vioe	protein	181	7% helix, 52% strand	Q7NSZ5
D	Hypothetical protein vioe	protein	179	7% helix, 55% strand	Q7NSZ5
E	Hypothetical protein vioe	protein	177	7% helix, 54% strand	Q7NSZ5
F	Hypothetical protein vioe	protein	183	7% helix, 52% strand	Q7NSZ5

Ligands and binding sites

PPY · 3-phenylpyruvic acid · ligand · 12 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	931	0.82	0.83	92	PPY
2	990	0.74	0.78	111	empty
3	152	0.68	0.88	34	empty
4	173	0.67	0.86	27	PPY
5	302	0.65	0.81	38	PPY

Interfaces

6 interfaces between chains.

A–B · 1785 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1776 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1650 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 345 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 178 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2ZF4 · Crystal Structure of VioE complexed with phenylpyruvic acid · the same entry in another collection · 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 Q7NSZ5
Elsewhere: RCSB PDB 2ZF4 · PDBe 2ZF4 · UniProt Q7NSZ5

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