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MolNFT v1 · #38910 · protein + DNA

Structure of transcription factor GENESIS/DNA complex

2HDC · DNA (5'- D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP…: “Structure of transcription factor GENESIS/DNA complex”. Solution nmr, 3 pockets (best druggability 0.46). MolNFT v1 #38910 on GenesisL1: 3D structure, binding sites and…

PDB
2HDC
Type
protein + DNA
Length
131 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3'); DNA (5'…
UniProt
Q63245
Pockets
3 · best druggability 0.46

Structure

solution nmr · 3 distinct chains · 48% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'- D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')dna17——
CDNA (5'- D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')dna17——
AProtein (transcription factor)protein9748% helix, 7% strandQ63245

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11490.460.7620empty
2800.330.7516empty
3560.270.7313empty

Interfaces

3 interfaces between chains.

  • C–A · 799 Ų buried · 19 hydrogen bonds · protein-nucleic
  • B–A · 760 Ų buried · 22 hydrogen bonds · protein-nucleic
  • B–C · 756 Ų buried · 64 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2HDC · Structure of transcription factor GENESIS/DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
  • Q63245 · AlphaFold monomer V2.0 prediction for forkhead box protein D3 (Q63245) · a predicted model of the same protein · chain A against A, TM-score 0.66

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