MolNFT v1 · #102225 · protein + DNA
Structural basis for thymine glycosylase activity on T:O6-methylg mismatch by methyl-cpg binding domain protein 4: implications for roles of ARG468 in mismatch recognition and catalysis
4OFH · Methyl-cpg-binding domain protein 4: “Structural basis for thymine glycosylase activity on T:O6-methylg mismatch by methyl-cpg binding domain…”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.43). MolNFT v1 #102225…
- PDB
- 4OFH
- 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; 12-mer DNA(T); 12-mer DNA(O6MEG)
- EC
- 3.2.2.-
- UniProt
- O95243
- Ligands
- MG
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-cpg-binding domain protein 4 (EC 3.2.2.-) | protein | 141 | 66% helix, 0% strand | O95243 |
| C | 12-mer DNA(T) | dna | 12 | — | — |
| D | 12-mer DNA(O6MEG) | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
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 | 84 | 0.43 | 0.80 | 17 | empty |
| 2 | 54 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 751 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 546 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–D · 423 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4OFH · Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG… · 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 4OFH · PDBe 4OFH · UniProt O95243
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