Research workbench
Crystal structure of old yellow enzyme from pichia sp. AKU4542
Analyse Crystal structure of old yellow enzyme from pichia sp. AKU4542 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AGZ
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Old yellow enzyme
- Ligands
- FMN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Old yellow enzyme | protein | 386 | 40% helix, 14% strand | — |
| B | Old yellow enzyme | protein | 386 | 40% helix, 15% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.67 | 0.80 | 42 | FMN |
| 2 | 326 | 0.63 | 0.79 | 36 | FMN |
| 3 | 60 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6AGZ · Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 · 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
- Elsewhere: RCSB PDB 6AGZ · PDBe 6AGZ
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