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MolNFT v1 · #10850 · protein + DNA

3D solution NMR structure of the wild type hmg-box domain of the human male sex determining factor sry complexed to DNA

1J46 · 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3': “3D solution NMR structure of the wild type hmg-box domain of the human male sex determining factor sry…”. Solution nmr, 2 pockets (best druggability 0.45). MolNFT v1 #10850 on…

PDB
1J46
Type
protein + DNA
Length
113 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3'…
UniProt
Q05066
Pockets
2 · best druggability 0.45

Structure

solution nmr · 3 distinct chains · 58% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3'dna14——
C5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)-3'dna14——
ASex-determining region Y proteinprotein8558% helix, 0% strandQ05066

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1870.450.8117empty
2710.310.7510empty

Interfaces

3 interfaces between chains.

  • B–A · 876 Ų buried · 10 hydrogen bonds · protein-nucleic
  • C–A · 776 Ų buried · 16 hydrogen bonds · protein-nucleic
  • B–C · 669 Ų buried · 45 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1J46 · 3D Solution NMR Structure of the Wild Type HMG-BOX Domain of the Human Male Sex… · the same entry in another collection · chain B against B, TM-score 1.00
  • Q05066 · AlphaFold monomer V2.0 prediction for sex-determining region Y protein (Q05066) · a predicted model of the same protein · chain A against A, TM-score 0.88

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