Research workbench
Crystal structure of methyl cpg binding domain of MBD4 in complex with the 5MCG/5MCG sequence
Analyse Crystal structure of 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
- 3VXX
- Type
- protein + DNA
- Length
- 91 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(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP…
- EC
- 3.2.2.-
- UniProt
- Q9Z2D7
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 63 | 22% helix, 22% strand | Q9Z2D7 |
| B | DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)- 3') | dna | 14 | — | — |
| C | DNA (5'-D(*GP*TP*CP*(5CM)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)- 3') | dna | 14 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, B
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 | 323 | 0.65 | 0.81 | 32 | ACT, EDO |
Interfaces
3 interfaces between chains.
- B–C · 580 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 400 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 315 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3VXX · Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG… · 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 0.65
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 3VXX · PDBe 3VXX · UniProt Q9Z2D7
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