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Crystal structure of hyp-1 protein from hypericum perforatum (st JOHN'S wort) involved in hypericin biosynthesis
Analyse Crystal structure of hyp-1 protein from hypericum perforatum (st JOHN'S wort)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IE5
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenolic oxidative coupling protein hyp-1
- UniProt
- Q8H1L1
- Ligands
- CL
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenolic oxidative coupling protein hyp-1 | protein | 160 | 30% helix, 42% strand | Q8H1L1 |
| B | Phenolic oxidative coupling protein hyp-1 | protein | 164 | 31% helix, 43% strand | Q8H1L1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B
- PGE · Triethylene glycol · additive · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.82 | 0.88 | 46 | 1PE, PG4, PEG |
| 2 | 921 | 0.81 | 0.82 | 89 | PGE, PG4 |
| 3 | 60 | 0.38 | 0.79 | 12 | 1PE |
| 4 | 58 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 608 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3IE5 · Crystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in… · 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 Q8H1L1
- Elsewhere: RCSB PDB 3IE5 · PDBe 3IE5 · UniProt Q8H1L1
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