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Nitroalkane oxidase: MUTANT402N crystallized with nitroethane

Analyse Nitroalkane oxidase: MUTANT402N crystallized with nitroethane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FCJ
Type: protein
Length: 1,724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitroalkane oxidase
UniProt: Q8X1D8
Ligands: FAD, NIE
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitroalkane oxidase	protein	431	53% helix, 12% strand	Q8X1D8
C	Nitroalkane oxidase	protein	430	54% helix, 12% strand	Q8X1D8
D	Nitroalkane oxidase	protein	432	53% helix, 12% strand	Q8X1D8

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
NIE · nitroethane · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, C, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.86	0.91	76	FAD, NIE, GOL
2	625	0.86	0.90	87	FAD, NIE, GOL
3	647	0.85	0.90	86	FAD, NIE, GOL
4	740	0.85	0.88	95	FAD, NIE, GOL
5	1073	0.82	0.83	73	empty

Interfaces

6 interfaces between chains.

A–C · 2732 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 2731 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2155 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2135 Å² buried · 29 hydrogen bonds · protein-protein
A–D · 204 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3FCJ · Nitroalkane oxidase: mutant402N crystallized with nitroethane · the same entry in another collection · chain A against A, TM-score 1.00
Q8X1D8 · AlphaFold monomer V2.0 prediction for nitroalkane oxidase (Q8X1D8) · a predicted model of the same protein · 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 Q8X1D8
Elsewhere: RCSB PDB 3FCJ · PDBe 3FCJ · UniProt Q8X1D8

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