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Solution structure of the methyl-cpg-binding domain of human MBD1 in complex with methylated DNA

Analyse Solution structure of the methyl-cpg-binding domain of human MBD1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1IG4
Type
protein + DNA
Length
99 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'; Methyl-cpg binding protein
UniProt
Q9UIS9
Pockets
1 · best druggability 0.40

Structure

solution nmr · 2 distinct chains · 11% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B, C5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'dna12——
AMethyl-cpg binding proteinprotein7511% helix, 23% strandQ9UIS9

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1760.400.7915empty

Interfaces

3 interfaces between chains.

  • B–C · 569 Ų buried · 53 hydrogen bonds · nucleic-nucleic
  • B–A · 523 Ų buried · 16 hydrogen bonds · protein-nucleic
  • C–A · 280 Ų buried · 7 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 1IG4 · Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with… · the same entry in another collection · chain B against B, TM-score 1.00
  • Q9UIS9 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 1 (Q9UIS9) · a predicted model of the same protein · chain A against A, TM-score 0.78

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