MolNFT v1 · #111784 · protein
Recombinantly expressed latent aurone synthase (polyphenol oxidase) co-crystallized with HEXATUNGSTOTELLURATE(VI) and soaked in H2O2
4Z13: “Recombinantly expressed latent aurone synthase (polyphenol oxidase) co-crystallized with…”. X-ray diffraction, 5 ligands (TEW, W, CU), 14 pockets (best druggability 0.82). MolNFT v1 #111784 on GenesisL1: 3D structure, binding sites…
- PDB
- 4Z13
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aurone synthase
- UniProt
- A0A075DN54
- Ligands
- TEW, W, CU, O, TE
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurone synthase | protein | 509 | 28% helix, 19% strand | A0A075DN54 |
| B | Aurone synthase | protein | 499 | 28% helix, 20% strand | A0A075DN54 |
Ligands and binding sites
- TEW · 6-tungstotellurate(VI) · ligand · 2 copies · chains A, B
- W · Tungsten ion · metal · 7 copies · chains A, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B
- O · Oxygen atom · ion · 4 copies · chains A, B
- TE · Tellurium · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.82 | 0.86 | 64 | empty |
| 2 | 146 | 0.59 | 0.84 | 22 | empty |
| 3 | 163 | 0.58 | 0.82 | 21 | empty |
| 4 | 70 | 0.48 | 0.83 | 12 | empty |
| 5 | 134 | 0.45 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 779 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4Z13 · Recombinantly expressed latent aurone synthase (polyphenol oxidase) co-crystallized with… · 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 A0A075DN54
- Elsewhere: RCSB PDB 4Z13 · PDBe 4Z13 · UniProt A0A075DN54
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