Research workbench
Pyranose 2-oxidase F454N mutant in complex with 2FG
Analyse Pyranose 2-oxidase F454N mutant in complex with 2FG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K4L
- Type
- protein
- Length
- 1,134 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose 2-oxidase
- EC
- 1.1.3.10
- UniProt
- Q7ZA32
- Ligands
- FAD, SHG
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 567 | 25% helix, 24% strand | Q7ZA32 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SHG · 2-deoxy-2-fluoro-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.87 | 0.92 | 77 | FAD, SHG |
| 2 | 611 | 0.86 | 0.91 | 70 | FAD, SHG |
| 3 | 903 | 0.78 | 0.80 | 74 | empty |
| 4 | 721 | 0.77 | 0.82 | 71 | empty |
| 5 | 304 | 0.72 | 0.85 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2718 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3K4L · Pyranose 2-oxidase F454N mutant in complex with 2FG · 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 Q7ZA32
- Elsewhere: RCSB PDB 3K4L · PDBe 3K4L · UniProt Q7ZA32
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