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Hcgas-16BP dsdna complex

Analyse Hcgas-16BP dsdna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6EDC
Type
protein + DNA
Length
379 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cyclic gmp-AMP synthase; DNA (5'- D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*A)-3'…
EC
2.7.7.86
UniProt
Q8N884
Ligands
ZN
Pockets
6 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACyclic gmp-AMP synthase (EC 2.7.7.86)protein34745% helix, 18% strandQ8N884
BDNA (5'- D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*A)-3')dna17——
CDNA (5'-D(*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)- 3')dna15——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11010.760.9714empty
29040.730.7854empty
35640.720.8051empty
44260.650.7829empty
5810.350.7517empty

Interfaces

3 interfaces between chains.

  • B–C · 715 Ų buried · 75 hydrogen bonds · nucleic-nucleic
  • A–B · 555 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–C · 392 Ų buried · 7 hydrogen bonds · protein-nucleic

Compared structures

  • 6EDC · hcGAS-16bp dsDNA complex · the same entry in another collection · chain A against A, TM-score 1.00
  • Q8N884 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8N884) · a predicted model of the same protein · chain A against A, TM-score 0.99

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