MolNFT v1 · #142124 · protein
Effect of mutation (R554A) on FAD modification in aspergillus oryzae RIB40FORMATE oxidase
5ZU2: “Effect of mutation (R554A) on FAD modification in aspergillus oryzae RIB40FORMATE oxidase”. X-ray diffraction, 1 ligand (FAD), 14 pockets (best druggability 0.86). MolNFT v1 #142124 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZU2
- 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
- FAD
- Pockets
- 14 · best druggability 0.86
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
- FAD · Flavin-adenine dinucleotide · 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.86 | 0.96 | 66 | FAD |
| 2 | 393 | 0.85 | 0.93 | 74 | FAD |
| 3 | 439 | 0.84 | 0.91 | 77 | FAD |
| 4 | 1120 | 0.77 | 0.79 | 106 | empty |
| 5 | 373 | 0.71 | 0.83 | 62 | empty |
Interfaces
3 interfaces between chains.
- B–C · 897 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 840 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5ZU2 · Effect of mutation (R554A) 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 5ZU2 · PDBe 5ZU2 · UniProt Q2UD26
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