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Structure of SOX18-HMG/PROX1-DNA

Analyse Structure of SOX18-HMG/PROX1-DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4Y60
Type
protein + DNA
Length
109 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcription factor sox-18; DNA (5'- D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*CP*TP*GP*GP*G…
UniProt
P43680
Pockets
4 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
CTranscription factor sox-18protein7667% helix, 0% strandP43680
ADNA (5'- D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*CP*TP*GP*GP*G)-3')dna17——
BDNA (5'- D(*GP*CP*CP*CP*AP*GP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*T)-3')dna16——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11330.520.8122empty
2640.350.7819empty
3560.290.757empty
4780.270.7111empty

Interfaces

3 interfaces between chains.

  • A–B · 708 Ų buried · 60 hydrogen bonds · nucleic-nucleic
  • C–B · 692 Ų buried · 13 hydrogen bonds · protein-nucleic
  • C–A · 669 Ų buried · 16 hydrogen bonds · protein-nucleic

Compared structures

  • 4Y60 · Structure of SOX18-HMG/PROX1-DNA · the same entry in another collection · chain C against C, TM-score 1.00
  • P43680 · AlphaFold monomer V2.0 prediction for transcription factor sox-18 (P43680) · a predicted model of the same protein · chain C against A, TM-score 0.96

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