Research workbench
Crystal structure of the methyl cpg binding domain of MBD4 in complex with the 5MCG/TG sequence in space group P1
Analyse Crystal structure of the methyl cpg binding domain of MBD4 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VYQ
- Type
- protein + DNA
- Length
- 147 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 4; DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3')…
- EC
- 3.2.2.-
- UniProt
- Q9Z2D7
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 63 | 21% helix, 22% strand | Q9Z2D7 |
| B | DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.67 | 0.81 | 32 | empty |
| 2 | 171 | 0.48 | 0.77 | 25 | empty |
| 3 | 120 | 0.37 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 547 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 434 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- A–B · 355 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 334 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3VYQ · Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Z2D7 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 4 (Q9Z2D7) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9Z2D7
- Elsewhere: RCSB PDB 3VYQ · PDBe 3VYQ · UniProt Q9Z2D7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.