Research workbench
Crystal structure of MBD4 catalytic domain bound to abasic DNA
Analyse Crystal structure of MBD4 catalytic domain bound to abasic DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DK9
- Type
- protein + DNA
- Length
- 162 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'; 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'…
- EC
- 3.2.2.-
- UniProt
- O95243
- Ligands
- K
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3' | dna | 11 | — | — |
| C | 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3' | dna | 11 | — | — |
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 140 | 61% helix, 0% strand | O95243 |
Ligands and binding sites
- K · Potassium ion · metal · chains C, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.57 | 0.86 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–A · 568 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 470 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- B–A · 403 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DK9 · Crystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA · the same entry in another collection · chain B against B, 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 4DK9 · PDBe 4DK9 · UniProt O95243
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