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MolNFT v1 · #106554 · protein + DNA

Crystal structure of hmg domain of the chondrogenesis master regulator, SOX9 in complex with chip-seq identified DNA element

4S2Q · DNA (5'- D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)…: “Crystal structure of hmg domain of the chondrogenesis master regulator, SOX9 in complex with chip-seq…”. X-ray diffraction, 3 pockets (best druggability 0.51). MolNFT…

PDB
4S2Q
Type
protein + DNA
Length
108 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3'); DNA (5'…
UniProt
Q04887
Pockets
3 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'- D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3')dna16——
BDNA (5'- D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')dna16——
DTranscription factor sox-9protein7666% helix, 0% strandQ04887

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11340.510.8024empty
21070.330.7311empty
3530.280.7512empty

Interfaces

3 interfaces between chains.

  • A–D · 734 Ų buried · 15 hydrogen bonds · protein-nucleic
  • B–D · 681 Ų buried · 12 hydrogen bonds · protein-nucleic
  • A–B · 654 Ų buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

  • 4S2Q · Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q04887 · AlphaFold monomer V2.0 prediction for transcription factor sox-9 (Q04887) · a predicted model of the same protein · chain D against A, TM-score 0.92

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