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MolNFT v1 · #80618 · protein + DNA

Structure of the SOX4 hmg domain bound to DNA

3U2B · DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)…: “Structure of the SOX4 hmg domain bound to DNA”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #80618 on GenesisL1: 3D structure, binding sites and…

PDB
3U2B
Type
protein + DNA
Length
108 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)- 3'); DNA…
UniProt
Q06831
Pockets
3 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)- 3')dna16——
BDNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)- 3')dna16——
CTranscription factor sox-4protein7664% helix, 0% strandQ06831

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11240.520.8122empty
2890.350.7612empty
31050.320.7213empty

Interfaces

3 interfaces between chains.

  • B–C · 772 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–B · 706 Ų buried · 70 hydrogen bonds · nucleic-nucleic
  • A–C · 641 Ų buried · 11 hydrogen bonds · protein-nucleic

Compared structures

  • 3U2B · Structure of the Sox4 HMG domain bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q06831 · AlphaFold monomer V2.0 prediction for transcription factor sox-4 (Q06831) · a predicted model of the same protein · chain C against A, TM-score 0.93

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