Research workbench
Crystal structure of pfhppd-Y13287 complex
Analyse Crystal structure of pfhppd-Y13287 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 853 Ų buried · 25 hydrogen bonds · protein-protein
- C–H · 847 Ų buried · 21 hydrogen bonds · protein-protein
- B–H · 707 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 705 Ų 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.