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Crystal structure of irf-3 bound to the prdiii-I regulatory element of the human interferon-B enhancer

Analyse Crystal structure of irf-3 bound to the prdiii-I regulatory element of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PI0
Type: protein + DNA
Length: 485 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interferon regulatory factor 3; Prdiii-I region of human interferon-B promoter strand 1…
UniProt: Q14653
Pockets: 14 · best druggability 0.66

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interferon regulatory factor 3	protein	98	34% helix, 20% strand	Q14653
B	Interferon regulatory factor 3	protein	112	32% helix, 20% strand	Q14653
C	Interferon regulatory factor 3	protein	107	33% helix, 21% strand	Q14653
D	Interferon regulatory factor 3	protein	104	31% helix, 21% strand	Q14653
E	Prdiii-I region of human interferon-B promoter strand 1	dna	32	—	—
F	Prdiii-I region of human interferon-B promoter strand 2	dna	32	—	—

Pockets

14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	409	0.66	0.80	47	empty
2	318	0.57	0.77	40	empty
3	213	0.49	0.76	24	empty
4	180	0.44	0.74	29	empty
5	57	0.40	0.81	15	empty

Interfaces

11 interfaces between chains.

E–F · 1420 Å² buried · 141 hydrogen bonds · nucleic-nucleic
D–F · 755 Å² buried · 13 hydrogen bonds · protein-nucleic
B–F · 721 Å² buried · 11 hydrogen bonds · protein-nucleic
C–F · 651 Å² buried · 9 hydrogen bonds · protein-nucleic
C–E · 569 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

2PI0 · Crystal Structure of IRF-3 bound to the PRDIII-I regulatory element of the human… · the same entry in another collection · chain F against F, TM-score 1.00
Q14653 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 3 (Q14653) · a predicted model of the same protein · chain C against A, TM-score 0.96

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
Elsewhere: RCSB PDB 2PI0 · PDBe 2PI0 · UniProt Q14653

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