Research workbench
Crystal structure MBD3 MBD domain in complex with methylated CpG DNA
Analyse Crystal structure MBD3 MBD domain in complex with methylated CpG DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CC8
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Methyl-CpG-binding domain protein 3; methylated CpG DNA
- UniProt
- O95983
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyl-CpG-binding domain protein 3 | protein | 71 | 11% helix, 32% strand | O95983 |
| C, D, E, F | methylated CpG DNA | dna | 12 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 12 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.61 | 0.82 | 38 | UNX |
| 2 | 253 | 0.60 | 0.80 | 36 | UNX |
| 3 | 50 | 0.22 | 0.72 | 10 | empty |
Interfaces
7 interfaces between chains.
- E–F · 555 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- C–D · 550 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–C · 340 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 339 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 284 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6CC8 · Crystal structure MBD3 mbd domain in complex with methylated cpg DNA · the same entry in another collection · chain C against C, TM-score 1.00
- O95983 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 3 (O95983) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 O95983
- Elsewhere: RCSB PDB 6CC8 · PDBe 6CC8 · UniProt O95983
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