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MolNFT v1 · #60277 · protein + DNA

Structure of a homeodomain in complex with DNA

3CMY · Paired box protein pax-3: “Structure of a homeodomain in complex with DNA”. X-ray diffraction, 1 pocket (best druggability 0.39). MolNFT v1 #60277 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3CMY
Type
protein + DNA
Length
75 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Paired box protein pax-3; 5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC…
UniProt
P23760
Pockets
1 · best druggability 0.39

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
APaired box protein pax-3protein6068% helix, 0% strandP23760
B5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC )-3'dna8——
C5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*D G)-3'dna7——

Ligands and binding sites

  • EDO · 1,2-ethanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1700.390.7919empty

Interfaces

3 interfaces between chains.

  • A–B · 516 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–C · 395 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–C · 338 Ų buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

  • 3CMY · Structure of a homeodomain in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P23760 · AlphaFold monomer V2.0 prediction for paired box protein pax-3 (P23760) · a predicted model of the same protein · chain A against A, TM-score 0.91

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