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Crystal structure of NF90 tandem dsrbds with dsrna

Analyse Crystal structure of NF90 tandem dsrbds with dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5DV7
Type
protein + RNA
Length
173 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'- R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3'); RNA (5'…
UniProt
Q9Z1X4
Pockets
2 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 32% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ARNA (5'- R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')rna18——
BRNA (5'- R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')rna18——
CInterleukin enhancer-binding factor 3protein13735% helix, 32% strandQ9Z1X4

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16070.600.7344empty
2960.450.7921empty

Interfaces

3 interfaces between chains.

  • A–B · 839 Ų buried · 66 hydrogen bonds · nucleic-nucleic
  • B–C · 485 Ų buried · 11 hydrogen bonds · protein-nucleic
  • A–C · 379 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 5DV7 · Crystal Structure of NF90 tandem dsRBDs with dsRNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9Z1X4 · AlphaFold monomer V2.0 prediction for interleukin enhancer-binding factor 3 (Q9Z1X4) · a predicted model of the same protein · chain C against A, TM-score 0.80

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