Research workbench
Inactive aurone synthase (polyphenol oxidase) co-crystallized with 1, 4-resorcinol
Analyse Inactive aurone synthase (polyphenol oxidase) co-crystallized with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z10
- Type
- protein
- Length
- 2,131 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aurone synthase
- UniProt
- A0A075DN54
- Ligands
- RCO, CU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Aurone synthase | protein | 347 | 38% helix, 10% strand | A0A075DN54 |
| G, K | Aurone synthase | protein | 12 | 0% helix, 0% strand | A0A075DN54 |
| H | Aurone synthase | protein | 10 | 0% helix, 0% strand | A0A075DN54 |
| I, J, L | Aurone synthase | protein | 4 | 0% helix, 0% strand | A0A075DN54 |
| F | Aurone synthase | protein | 350 | 39% helix, 9% strand | A0A075DN54 |
Ligands and binding sites
- RCO · Resorcinol · ligand · 11 copies · chains A, D, G, C, B, H, J, F, I, E, K, L
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, F, E, C, D
- ACT · Acetate ion · additive · chains K, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.87 | 0.88 | 123 | RCO, GOL |
| 2 | 1065 | 0.86 | 0.87 | 134 | RCO, GOL, ACT |
| 3 | 1169 | 0.84 | 0.85 | 133 | RCO |
| 4 | 202 | 0.56 | 0.79 | 25 | empty |
| 5 | 81 | 0.50 | 0.83 | 20 | RCO |
Interfaces
23 interfaces between chains.
- B–F · 475 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 469 Ų buried · 14 hydrogen bonds · protein-protein
- E–K · 426 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 modified (disulfide, nonstandard).
Compared structures
- 4Z10 · Inactive aurone synthase (polyphenol oxidase) co-crystallized with 1,4-resorcinol · 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 4Z10 · PDBe 4Z10 · UniProt A0A075DN54
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