Research workbench
Effect of mutation (R554K) on FAD modification in aspergillus oryzae RIB40FORMATE oxidase
Analyse Effect of mutation (R554K) on FAD modification in aspergillus oryzae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZU3
- Type
- protein
- Length
- 1,731 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate oxidase
- UniProt
- Q2UD26
- Ligands
- FAY
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Formate oxidase | protein | 577 | 32% helix, 25% strand | Q2UD26 |
Ligands and binding sites
- FAY · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, C, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.85 | 0.96 | 50 | FAY |
| 2 | 280 | 0.85 | 0.96 | 55 | FAY |
| 3 | 280 | 0.85 | 0.96 | 48 | FAY |
| 4 | 539 | 0.79 | 0.85 | 67 | empty |
| 5 | 331 | 0.70 | 0.83 | 48 | MPD |
Interfaces
3 interfaces between chains.
- B–C · 874 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 861 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 501 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5ZU3 · Effect of mutation (R554K) on FAD modification in Aspergillus oryzae RIB40formate oxidase · 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 Q2UD26
- Elsewhere: RCSB PDB 5ZU3 · PDBe 5ZU3 · UniProt Q2UD26
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