Research workbench
Structure of the glycosylase domain of MBD4 bound to ap site containing DNA
Analyse Structure of the glycosylase domain of MBD4 bound to ap site containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E9F
- Type
- protein + DNA
- Length
- 162 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*(3DR)P*GP*CP*AP*GP*C)-3'…
- EC
- 3.2.2.-
- UniProt
- O95243
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 138 | 64% helix, 0% strand | O95243 |
| C | DNA (5'-D(*CP*CP*AP*GP*CP*GP*(3DR)P*GP*CP*AP*GP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.43 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 629 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–D · 552 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–D · 443 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4E9F · Structure of the glycosylase domain of MBD4 bound to AP site 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
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O95243
- Elsewhere: RCSB PDB 4E9F · PDBe 4E9F · UniProt O95243
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