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DHX36 in complex with the C-myc G-quadruplex

Analyse DHX36 in complex with the C-myc G-quadruplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5VHE
Type
protein + DNA
Length
895 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Deah (asp-glu-ala-his) box polypeptide 36; DNA (5'…
UniProt
Q05B79
Ligands
K
Pockets
18 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADeah (asp-glu-ala-his) box polypeptide 36protein87146% helix, 14% strandQ05B79
BDNA (5'- D(*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*TP* TP*T)-3')dna24——

Ligands and binding sites

  • K · Potassium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17480.880.9180empty
23260.810.9144empty
31570.780.9435empty
41530.620.8424empty
54500.610.7632empty

Interfaces

1 interface between chains.

  • A–B · 1882 Ų buried · 29 hydrogen bonds · protein-nucleic

Compared structures

  • 5VHE · DHX36 in complex with the c-Myc G-quadruplex · the same entry in another collection · chain A against A, TM-score 1.00
  • Q05B79 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA/RNA helicase DHX36 (Q05B79) · a predicted model of the same protein · chain A against A, TM-score 0.77

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