MolNFT v1 · #190475 · protein

Crystal structure of pfhppd-Y13287 complex

7X8E · 4-hydroxyphenylpyruvate dioxygenase: “Crystal structure of pfhppd-Y13287 complex”. X-ray diffraction, 2 ligands (92X, CO), 20 pockets (best druggability 0.83). MolNFT v1 #190475 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7X8E
Type: protein
Length: 2,701 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxyphenylpyruvate dioxygenase
UniProt: A0A0W0HIR1
Ligands: 92X, CO
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	4-hydroxyphenylpyruvate dioxygenase	protein	341	27% helix, 34% strand	A0A0W0HIR1
B	4-hydroxyphenylpyruvate dioxygenase	protein	341	28% helix, 34% strand	A0A0W0HIR1
D	4-hydroxyphenylpyruvate dioxygenase	protein	340	28% helix, 34% strand	A0A0W0HIR1
E, H	4-hydroxyphenylpyruvate dioxygenase	protein	335	27% helix, 33% strand	A0A0W0HIR1
F	4-hydroxyphenylpyruvate dioxygenase	protein	336	29% helix, 33% strand	A0A0W0HIR1
G	4-hydroxyphenylpyruvate dioxygenase	protein	332	27% helix, 32% strand	A0A0W0HIR1

Ligands and binding sites

92X · 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2, 4-dione · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1167	0.83	0.84	106	empty
2	935	0.80	0.82	67	empty
3	142	0.77	0.94	28	empty
4	155	0.75	0.92	25	empty
5	126	0.74	0.93	25	empty

Interfaces

11 interfaces between chains.

A–E · 859 Å² buried · 19 hydrogen bonds · protein-protein
B–F · 853 Å² buried · 25 hydrogen bonds · protein-protein
C–H · 847 Å² buried · 21 hydrogen bonds · protein-protein
B–H · 707 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 705 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7X8E · Crystal structure of PfHPPD-Y13287 complex · the same entry in another collection · chain E against E, 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 A0A0W0HIR1
Elsewhere: RCSB PDB 7X8E · PDBe 7X8E · UniProt A0A0W0HIR1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.