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Solution structure of the dead ringer arid-DNA complex

Analyse Solution structure of the dead ringer arid-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1KQQ
Type
protein + DNA
Length
161 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'…
UniProt
Q24573
Pockets
4 · best druggability 0.53

Structure

solution nmr · 3 distinct chains · 66% helix, 2% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'dna15——
C5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'dna15——
ADead ringer proteinprotein13166% helix, 2% strandQ24573

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13420.530.7422empty
21660.510.7816empty
31010.410.7715empty
4540.290.7412empty

Interfaces

3 interfaces between chains.

  • B–C · 731 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • C–A · 439 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–A · 438 Ų buried · 12 hydrogen bonds · protein-nucleic

Compared structures

  • 1KQQ · Solution Structure of the Dead ringer ARID-DNA Complex · the same entry in another collection · chain B against B, TM-score 1.00
  • Q24573 · AlphaFold monomer V2.0 prediction for protein dead ringer (Q24573) · a predicted model of the same protein · chain A against A, TM-score 0.91

Analyse

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