MolNFT v1 · #161430 · protein + DNA

DNA binding domain of lux arrythmo in complex with DNA

6QEC · DNA (5'- D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*C…: “DNA binding domain of lux arrythmo in complex with DNA”. X-ray diffraction, 2 pockets (best druggability 0.35). MolNFT v1 #161430 on GenesisL1: 3D structure, binding…

PDB: 6QEC
Type: protein + DNA
Length: 85 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3'); Transcription…
UniProt: Q9SNB4
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U	DNA (5'- D(APTPTPCPGPAPAPTPAPTTPAPTPAPTPTPCPGPAPA)-3')	dna	10	—	—
B	DNA (5'- D(APTPTPCPGPAPAPTPAPTTPAPTPAPTPTPCPGPAPA)-3')	dna	10	—	—
A	Transcription factor lux	protein	65	65% helix, 0% strand	Q9SNB4

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

2 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	111	0.35	0.73	16	empty
2	50	0.30	0.76	10	empty

Interfaces

3 interfaces between chains.

B–A · 417 Å² buried · 7 hydrogen bonds · protein-nucleic
U–B · 402 Å² buried · 28 hydrogen bonds · nucleic-nucleic
U–A · 367 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6QEC · DNA binding domain of LUX ARRYTHMO in complex with DNA · the same entry in another collection · chain U against U, TM-score 1.00
Q9SNB4 · AlphaFold monomer V2.0 prediction for transcription factor lux (Q9SNB4) · a predicted model of the same protein · chain A against A, TM-score 0.81

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 Q9SNB4
Elsewhere: RCSB PDB 6QEC · PDBe 6QEC · UniProt Q9SNB4

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