Research workbench
Cpg specific methyltransferase in complex with target DNA
Analyse Cpg specific methyltransferase in complex with target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DKJ
- Type
- protein + DNA
- Length
- 416 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosine-specific methyltransferase; DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP…
- EC
- 2.1.1.37
- UniProt
- Q8EVR5
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosine-specific methyltransferase (EC 2.1.1.37) | protein | 388 | 38% helix, 19% strand | Q8EVR5 |
| B | DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)- 3') | dna | 14 | — | — |
| C | DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)- 3') | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.77 | 0.93 | 36 | SAH |
| 2 | 541 | 0.70 | 0.80 | 56 | GOL |
| 3 | 267 | 0.62 | 0.81 | 31 | empty |
| 4 | 135 | 0.57 | 0.83 | 22 | empty |
| 5 | 89 | 0.35 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1024 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 761 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 608 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4DKJ · CpG specific methyltransferase in complex with target DNA · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8EVR5
- Elsewhere: RCSB PDB 4DKJ · PDBe 4DKJ · UniProt Q8EVR5
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