MolNFT v1 · #46493 · protein + DNA

Crystal structure of nfkb, IRF7, IRF3 bound to the interferon-B enhancer

2O61 · 36-mer: “Crystal structure of nfkb, IRF7, IRF3 bound to the interferon-B enhancer”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #46493 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2O61
Type: protein + DNA
Length: 882 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 36-mer; 34-mer; Transcription factor P65/INTERFERON regulatory factor 7/INTERFERON…
UniProt: Q04206, Q92985, Q14653, P19838
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	36-mer	dna	36	—	—
F	34-mer	dna	34	—	—
A	Transcription factor P65/INTERFERON regulatory factor 7/INTERFERON regulatory factor 3 fusion protein	protein	498	19% helix, 29% strand	Q04206, Q92985, Q14653
B	Nuclear factor nf-kappa-B P105 subunit	protein	314	13% helix, 36% strand	P19838

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1035	0.84	0.86	104	empty
2	551	0.65	0.77	45	empty
3	107	0.65	0.89	27	empty
4	70	0.57	0.88	20	empty
5	76	0.56	0.87	21	empty

Interfaces

6 interfaces between chains.

E–A · 1642 Å² buried · 31 hydrogen bonds · protein-nucleic
F–A · 1544 Å² buried · 32 hydrogen bonds · protein-nucleic
E–F · 1490 Å² buried · 142 hydrogen bonds · nucleic-nucleic
A–B · 810 Å² buried · 17 hydrogen bonds · protein-protein
F–B · 591 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

2O61 · Crystal Structure of NFkB, IRF7, IRF3 bound to the interferon-b enhancer · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.96
Q04206 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04206) · a predicted model of the same protein · chain A against A, TM-score 0.56
Q14653 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 3 (Q14653) · a predicted model of the same protein · chain A against A, TM-score 0.23
Q92985 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 7 (Q92985) · a predicted model of the same protein · chain A against A, TM-score 0.23

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 Q04206
Every structure of UniProt Q92985
Every structure of UniProt Q14653
Every structure of UniProt P19838
Elsewhere: RCSB PDB 2O61 · PDBe 2O61 · UniProt Q04206 · UniProt Q92985 · UniProt Q14653 · UniProt P19838

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