MolNFT v1 · #22102 · protein + DNA

Nfkb P50 homodimer bound to DNA

1SVC · DNA (5'- D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*…: “Nfkb P50 homodimer bound to DNA”. X-ray diffraction, 2 pockets (best druggability 0.44). MolNFT v1 #22102 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SVC
Type: protein + DNA
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3'); Protein…
UniProt: P19838
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	DNA (5'- D(APGPAPTPGPGPGPGPAPAPTPCPCPCPCPTPA PGP*A)-3')	dna	19	—	—
P	Protein (nuclear factor kappa-B (nf-kb))	protein	311	18% helix, 37% strand	P19838

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	56	0.44	0.83	18	empty
2	67	0.37	0.78	21	empty

Interfaces

1 interface between chains.

D–P · 653 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

1SVC · Nfkb P50 homodimer bound to DNA · the same entry in another collection · chain D against D, TM-score 1.00
P19838 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P19838) · a predicted model of the same protein · chain P against A, TM-score 0.97

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 P19838
Elsewhere: RCSB PDB 1SVC · PDBe 1SVC · UniProt P19838

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