Research workbench
Crystal structure of athppd-lancotrione complex
Analyse Crystal structure of athppd-lancotrione complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X5R
- Type
- protein
- Length
- 386 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
- 9P5, BCN, CO
- Pockets
- 2 · best druggability 0.69
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 | 386 | 30% helix, 33% strand | P93836 |
Ligands and binding sites
- 9P5 · (1R,3R)-2-[(S)-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl) ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol · ligand · chains A
- BCN · Bicine · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.69 | 0.80 | 53 | CO, 9P5, BCN |
| 2 | 74 | 0.36 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7X5R · Crystal structure of AtHPPD-Lancotrione 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 7X5R · PDBe 7X5R · UniProt P93836
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