Research workbench
Mouse MBD4 glycosylase domain in complex with a G:5HMU (5- hydroxymethyluracil) mismatch
Analyse Mouse MBD4 glycosylase domain in complex with a G:5HMU (5- hydroxymethyluracil)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EW0
- Type
- protein + DNA
- Length
- 165 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(*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- Q9Z2D7
- Ligands
- NI
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 143 | 62% helix, 0% strand | Q9Z2D7 |
| B | DNA (5'-D(*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*CP*CP*AP*TP*GP*(5HU)P*GP*CP*TP*GP*A)-3') | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.46 | 0.80 | 17 | empty |
| 2 | 73 | 0.31 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 759 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 498 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–B · 360 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4EW0 · mouse MBD4 glycosylase domain in complex with a G:5hmU (5-hydroxymethyluracil) mismatch · 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 0.99
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 Q9Z2D7
- Elsewhere: RCSB PDB 4EW0 · PDBe 4EW0 · UniProt Q9Z2D7
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