Research workbench

Podospora anserina nitroalkane oxidase

Analyse Podospora anserina nitroalkane oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MKH
Type: protein
Length: 1,704 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitroalkane oxidase
EC: 1.7.3.1
UniProt: B2AM55
Ligands: FAD, MG, SO4
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nitroalkane oxidase (EC 1.7.3.1)	protein	426	56% helix, 12% strand	B2AM55

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

8 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	997	0.85	0.86	107	FAD
2	1067	0.84	0.85	122	FAD
3	1098	0.84	0.85	119	FAD
4	1068	0.84	0.85	114	FAD
5	986	0.82	0.83	95	empty

Interfaces

6 interfaces between chains.

B–C · 2879 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 2878 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 2102 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 2100 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 178 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3MKH · Podospora anserina Nitroalkane Oxidase · the same entry in another collection · chain A against A, TM-score 1.00
B2AM55 · AlphaFold monomer V2.0 prediction for nitroalkane oxidase (B2AM55) · 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 B2AM55
Elsewhere: RCSB PDB 3MKH · PDBe 3MKH · UniProt B2AM55

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