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Protein domain complex with ssdna

Analyse Protein domain complex with ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4QGU
Type
protein + DNA
Length
404 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Gamma-interferon-inducible protein 16; DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')
UniProt
Q16666
Pockets
3 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 49% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AGamma-interferon-inducible protein 16protein19111% helix, 50% strandQ16666
BGamma-interferon-inducible protein 16protein19112% helix, 49% strandQ16666
CDNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')dna12——
DDNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110360.760.7977empty
25570.700.7946empty
3820.280.7217empty

Interfaces

4 interfaces between chains.

  • C–D · 575 Ų buried · 30 hydrogen bonds · nucleic-nucleic
  • A–B · 551 Ų buried · 8 hydrogen bonds · protein-protein
  • B–C · 222 Ų buried · 5 hydrogen bonds · protein-nucleic
  • A–D · 180 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 4QGU · protein domain complex with ssDNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q16666 · AlphaFold monomer V2.0 prediction for gamma-interferon-inducible protein 16 (Q16666) · a predicted model of the same protein · chain A against A, TM-score 0.98

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