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Crystal structure of the paz domain of human EIF2C1 in complex with a 9-mer siRNA-like duplex of deoxynucleotide overhang

Analyse Crystal structure of the paz domain of human EIF2C1 in complex with a 9-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SI2
Type: protein + RNA
Length: 129 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'; Eukaryotic translation initiation factor 2C 1
UniProt: Q9UL18
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-R(CPGPUPGPAPCPU)-D(PCP*T)-3'	rna	9	—	—
A	Eukaryotic translation initiation factor 2C 1	protein	120	28% helix, 29% strand	Q9UL18

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.52	0.83	22	empty

Interfaces

1 interface between chains.

B–A · 856 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

1SI2 · Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like… · the same entry in another collection · chain B against B, TM-score 1.00
Q9UL18 · AlphaFold monomer V2.0 prediction for protein argonaute-1 (Q9UL18) · a predicted model of the same protein · chain A 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 Q9UL18
Elsewhere: RCSB PDB 1SI2 · PDBe 1SI2 · UniProt Q9UL18

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