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Crystal structure of a hmg domain of transcription factor sox-9 bound to DNA (sox-9/DNA) from homo sapiens at 2.77 a resolution

Analyse Crystal structure of a hmg domain of transcription factor sox-9 bound to DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4EUW
Type
protein + DNA
Length
96 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcription factor sox-9; DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3'); DNA…
UniProt
P48436
Pockets
1 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscription factor sox-9protein7268% helix, 0% strandP48436
BDNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')dna12——
CDNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')dna12——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1800.440.8120empty

Interfaces

3 interfaces between chains.

  • A–B · 609 Ų buried · 12 hydrogen bonds · protein-nucleic
  • A–C · 596 Ų buried · 10 hydrogen bonds · protein-nucleic
  • B–C · 537 Ų buried · 55 hydrogen bonds · nucleic-nucleic

Compared structures

  • 4EUW · Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA)… · the same entry in another collection · chain A against A, TM-score 1.00
  • P48436 · AlphaFold monomer V2.0 prediction for transcription factor sox-9 (P48436) · a predicted model of the same protein · chain A against A, TM-score 0.97

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