MolNFT v1 · #22348 · protein + DNA

Structure of the DNA binding domains of IRF3, atf-2 and jun bound to DNA

1T2K · 31-mer: “Structure of the DNA binding domains of IRF3, atf-2 and jun bound to DNA”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #22348 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1T2K
Type: protein + DNA
Length: 403 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 31-mer; Interferon regulatory factor 3; Transcription factor ap-1; Cyclic-AMP-dependent…
UniProt: Q14653, P05412, P15336
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	31-mer	dna	31	—	—
F	31-mer	dna	31	—	—
A	Interferon regulatory factor 3	protein	110	35% helix, 19% strand	Q14653
B	Interferon regulatory factor 3	protein	108	31% helix, 18% strand	Q14653
C	Transcription factor ap-1	protein	62	95% helix, 0% strand	P05412
D	Cyclic-AMP-dependent transcription factor atf-2	protein	61	95% helix, 0% strand	P15336

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	736	0.74	0.80	64	empty
2	463	0.74	0.83	32	empty
3	213	0.52	0.78	29	empty
4	137	0.52	0.81	25	empty
5	93	0.42	0.78	15	empty

Interfaces

12 interfaces between chains.

E–F · 1287 Å² buried · 125 hydrogen bonds · nucleic-nucleic
C–D · 1010 Å² buried · 2 hydrogen bonds · protein-protein
F–A · 708 Å² buried · 10 hydrogen bonds · protein-nucleic
F–B · 637 Å² buried · 9 hydrogen bonds · protein-nucleic
E–B · 538 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

1T2K · Structure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound To DNA · the same entry in another collection · chain D against D, TM-score 1.00
Q14653 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 3 (Q14653) · a predicted model of the same protein · chain B against A, TM-score 0.96
P15336 · AlphaFold monomer V2.0 prediction for cyclic AMP-dependent transcription factor atf-2… · a predicted model of the same protein · chain D against A, TM-score 0.87
P05412 · AlphaFold monomer V2.0 prediction for transcription factor ap-1 (P05412) · a predicted model of the same protein · chain C against A, TM-score 0.72

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 Q14653
Every structure of UniProt P05412
Every structure of UniProt P15336
Elsewhere: RCSB PDB 1T2K · PDBe 1T2K · UniProt Q14653 · UniProt P05412 · UniProt P15336

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