GL1X · GenesisL1 explorer

MolNFT v1 · #63190 · protein + DNA

Structure of SOX17 bound to DNA

3F27 · DNA (5'- D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*…: “Structure of SOX17 bound to DNA”. X-ray diffraction, 3 pockets (best druggability 0.49). MolNFT v1 #63190 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3F27
Type
protein + DNA
Length
106 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)- 3'); DNA…
UniProt
Q61473
Pockets
3 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'- D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)- 3')dna16——
BDNA (5'- D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)- 3')dna16——
DTranscription factor sox-17protein7469% helix, 0% strandQ61473

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11310.490.7920empty
2620.360.7910empty
3530.350.7915empty

Interfaces

3 interfaces between chains.

  • A–D · 702 Ų buried · 15 hydrogen bonds · protein-nucleic
  • A–B · 694 Ų buried · 64 hydrogen bonds · nucleic-nucleic
  • B–D · 665 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 3F27 · Structure of Sox17 Bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q61473 · AlphaFold monomer V2.0 prediction for transcription factor sox-17 (Q61473) · a predicted model of the same protein · chain D against A, TM-score 0.93

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