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MolNFT v1 · #76491 · protein + DNA

Structural basis of selective binding of non-methylated cpg islands by the cxxc domain of CFP1

3QMG · Cpg-binding protein: “Structural basis of selective binding of non-methylated cpg islands by the cxxc domain of CFP1”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #76491 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3QMG
Type
protein + DNA
Length
76 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cpg-binding protein; 5'-D(*GP*CP*CP*AP*AP*CP*GP*GP*TP*GP*GP*C)-3'…
UniProt
Q9P0U4
Ligands
ZN

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACpg-binding proteinprotein5235% helix, 0% strandQ9P0U4
B5'-D(*GP*CP*CP*AP*AP*CP*GP*GP*TP*GP*GP*C)-3'dna12——
C5'-D(*GP*CP*CP*AP*CP*CP*GP*TP*TP*GP*GP*C)-3'dna12——

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A
  • PEG · Di(hydroxyethyl)ether · additive · chains A

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

Interfaces

3 interfaces between chains.

  • B–C · 548 Ų buried · 64 hydrogen bonds · nucleic-nucleic
  • A–B · 373 Ų buried · 8 hydrogen bonds · protein-nucleic
  • A–C · 279 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 3QMG · Structural Basis of Selective Binding of Non-Methylated CpG islands by the CXXC Domain of… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9P0U4 · AlphaFold monomer V2.0 prediction for cxxc-type zinc finger protein 1 (Q9P0U4) · a predicted model of the same protein · chain A against A, TM-score 0.96

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