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Structure of glycosylase domain of MBD4 bound to 5HMU containing DNA

Analyse Structure of glycosylase domain of MBD4 bound to 5HMU containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4E9H
Type
protein + DNA
Length
161 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Methyl-cpg-binding domain protein 4; DNA (5'-D(*CP*CP*AP*GP*CP*GP*(5HU)P*GP*CP*AP*GP*C)-3'…
EC
3.2.2.-
UniProt
O95243
Pockets
1 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMethyl-cpg-binding domain protein 4 (EC 3.2.2.-)protein13764% helix, 0% strandO95243
CDNA (5'-D(*CP*CP*AP*GP*CP*GP*(5HU)P*GP*CP*AP*GP*C)-3')dna12——
DDNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')dna12——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1740.410.8016empty

Interfaces

3 interfaces between chains.

  • A–C · 772 Ų buried · 25 hydrogen bonds · protein-nucleic
  • C–D · 549 Ų buried · 66 hydrogen bonds · nucleic-nucleic
  • A–D · 445 Ų buried · 12 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 4E9H · structure of glycosylase domain of MBD4 bound to 5hmU containing DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • O95243 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 4 (O95243) · a predicted model of the same protein · chain A against A, TM-score 0.99

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