Research workbench
Crystal structure of zmhppd-Y13161 complex
Analyse Crystal structure of zmhppd-Y13161 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X7L
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- UniProt
- A0A1D6H1G0
- Ligands
- 94L, CO
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase | protein | 364 | 27% helix, 35% strand | A0A1D6H1G0 |
| B | 4-hydroxyphenylpyruvate dioxygenase | protein | 363 | 27% helix, 36% strand | A0A1D6H1G0 |
| C | 4-hydroxyphenylpyruvate dioxygenase | protein | 376 | 28% helix, 36% strand | A0A1D6H1G0 |
| D | 4-hydroxyphenylpyruvate dioxygenase | protein | 367 | 26% helix, 36% strand | A0A1D6H1G0 |
Ligands and binding sites
- 94L · 3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2, 4-dione · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.85 | 0.87 | 150 | empty |
| 2 | 566 | 0.76 | 0.82 | 68 | CO, 94L |
| 3 | 370 | 0.69 | 0.82 | 49 | CO, 94L |
| 4 | 284 | 0.68 | 0.83 | 39 | CO, 94L |
| 5 | 292 | 0.68 | 0.83 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1550 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 188 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7X7L · Crystal structure of ZmHPPD-Y13161 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 A0A1D6H1G0
- Elsewhere: RCSB PDB 7X7L · PDBe 7X7L · UniProt A0A1D6H1G0
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