Research workbench

N, N-dimethylformamidase

Analyse N, N-dimethylformamidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LVV
Type: protein
Length: 7,096 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Paracoccus sp. SSG05
Molecule: N,N-dimethylformamidase large subunit; N,N-dimethylformamidase small subunit
EC: 3.5.1.56
UniProt: I6NT79, I6NWZ0
Ligands: FE
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · resolution 2.8 · 2 distinct chains · 21% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O	N,N-dimethylformamidase large subunit (EC 3.5.1.56)	protein	762	16% helix, 33% strand	I6NT79
B, D, F, H, J, L, N, P	N,N-dimethylformamidase small subunit (EC 3.5.1.56)	protein	125	49% helix, 14% strand	I6NWZ0

Ligands and binding sites

FE · Fe (III) ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	768	0.90	0.94	92	empty
2	816	0.90	0.93	99	empty
3	735	0.89	0.93	88	empty
4	758	0.89	0.93	89	empty
5	887	0.82	0.84	85	empty

Interfaces

31 interfaces between chains.

E–G · 2937 Å² buried · 25 hydrogen bonds · protein-protein
M–O · 2936 Å² buried · 24 hydrogen bonds · protein-protein
I–K · 2931 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 2914 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2073 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

6LVV · N, N-dimethylformamidase · 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 I6NT79
Every structure of UniProt I6NWZ0
Elsewhere: RCSB PDB 6LVV · PDBe 6LVV · UniProt I6NT79 · UniProt I6NWZ0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.