MolNFT v1 · #58528 · protein

Wrba from escherichia COLI, NADH complex

3B6J · Flavoprotein wrba: “Wrba from escherichia COLI, NADH complex”. X-ray diffraction, 3 ligands (FMN, NAD, AMP), 3 pockets (best druggability 0.44). MolNFT v1 #58528 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3B6J
Type: protein
Length: 394 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavoprotein wrba
UniProt: P0A8G6
Ligands: FMN, NAD, AMP
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Flavoprotein wrba	protein	197	39% helix, 19% strand	P0A8G6

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
AMP · Adenosine monophosphate · ligand · chains B
15P · Polyethylene glycol (N=34) · additive · 6 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.44	0.80	18	FMN
2	88	0.41	0.78	18	FMN
3	52	0.32	0.77	13	15P

Interfaces

1 interface between chains.

A–B · 1053 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3B6J · WrbA from Escherichia coli, NADH complex · the same entry in another collection · chain A against A, TM-score 1.00
P0A8G6 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase (quinone) (P0A8G6) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A8G6
Elsewhere: RCSB PDB 3B6J · PDBe 3B6J · UniProt P0A8G6

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