Research workbench
Structure of wild-type human MBD4 bound to a G:T mismatch
Analyse Structure of wild-type human MBD4 bound to a G:T mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CHZ
- Type
- protein + DNA
- Length
- 164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-cpg-binding domain protein 4; 7-mer DNA; 12-mer DNA(G); 5-mer DNA
- EC
- 3.2.2.-
- UniProt
- O95243
- Ligands
- MG
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 4 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 | 140 | 64% helix, 0% strand | O95243 |
| C | 7-mer DNA | dna | 7 | — | — |
| D | 12-mer DNA(G) | dna | 12 | — | — |
| B | 5-mer DNA | dna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.42 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 473 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 393 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 382 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 309 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- D–B · 228 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 5CHZ · Structure of wild-type human MBD4 bound to a G:T mismatch · 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 5CHZ · PDBe 5CHZ · UniProt O95243
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