Research workbench
Crystal structure of phaeospaeria nodrum fructosyl peptide oxidase mutant ASN56ALA in complexes with sodium and chloride ions
Analyse Crystal structure of phaeospaeria nodrum fructosyl peptide oxidase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XAO
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q0UIL6
- Ligands
- FAD, NA, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein | protein | 431 | 31% helix, 26% strand | Q0UIL6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 4 copies · chains A, C
- CL · Chloride ion · ion · 5 copies · chains A, C
- ACY · Acetic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.81 | 0.82 | 104 | FAD, ACY |
| 2 | 1141 | 0.80 | 0.82 | 103 | FAD, ACY |
| 3 | 97 | 0.69 | 0.92 | 21 | empty |
| 4 | 608 | 0.67 | 0.76 | 60 | empty |
| 5 | 65 | 0.50 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 338 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5XAO · Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in… · 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 Q0UIL6
- Elsewhere: RCSB PDB 5XAO · PDBe 5XAO · UniProt Q0UIL6
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