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Crystal structure of athppd-Y14240 complex

Analyse Crystal structure of athppd-Y14240 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7X5Y
Type: protein
Length: 381 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxyphenylpyruvate dioxygenase
EC: 1.13.11.27
UniProt: P93836
Ligands: HZS, CO
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)	protein	381	30% helix, 33% strand	P93836

Ligands and binding sites

HZS · (1R,3S)-5-methyl-2-[(1S)-2-naphthalen-1-yloxy-1-oxidanyl-ethyl]cyclohexane-1,3-diol · ligand · chains A
CO · Cobalt (II) ion · metal · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	494	0.70	0.80	43	HZS, MPD
2	70	0.34	0.76	15	MPD
3	50	0.24	0.72	13	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7X5Y · Crystal structure of AtHPPD-Y14240 complex · 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 P93836
Elsewhere: RCSB PDB 7X5Y · PDBe 7X5Y · UniProt P93836

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