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Imine reductase from myxococcus stipitatus V8 variant in complex with NAD+

Analyse Imine reductase from myxococcus stipitatus V8 variant in complex with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TOE
Type: protein
Length: 1,743 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coenzyme F420-dependent NADP oxidoreductase
UniProt: L7U9F5
Ligands: NAD
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Coenzyme F420-dependent NADP oxidoreductase	protein	292	56% helix, 12% strand	L7U9F5
B	Coenzyme F420-dependent NADP oxidoreductase	protein	293	56% helix, 12% strand	L7U9F5
D	Coenzyme F420-dependent NADP oxidoreductase	protein	286	54% helix, 13% strand	L7U9F5
E	Coenzyme F420-dependent NADP oxidoreductase	protein	289	55% helix, 12% strand	L7U9F5
F	Coenzyme F420-dependent NADP oxidoreductase	protein	291	56% helix, 12% strand	L7U9F5

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, E, B, F, C, D

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	896	0.83	0.85	102	empty
2	444	0.81	0.88	51	NAD
3	436	0.79	0.87	50	NAD
4	441	0.77	0.86	49	NAD
5	724	0.77	0.82	62	NAD

Interfaces

7 interfaces between chains.

A–E · 4555 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 4513 Å² buried · 33 hydrogen bonds · protein-protein
B–F · 4473 Å² buried · 33 hydrogen bonds · protein-protein
C–F · 249 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 84 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6TOE · Imine Reductase from Myxococcus stipitatus V8 variant in complex with NAD+ · 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 L7U9F5
Elsewhere: RCSB PDB 6TOE · PDBe 6TOE · UniProt L7U9F5

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