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

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
1SI3
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*UP*CP*U)-3'; Eukaryotic translation initiation factor 2C 1
UniProt
Q9UL18
Pockets
1 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3'rna9——
AEukaryotic translation initiation factor 2C 1protein12023% helix, 29% strandQ9UL18

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1990.570.8618empty

Interfaces

1 interface between chains.

  • B–A · 817 Ų buried · 21 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

  • 1SI3 · 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

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