Research workbench
Crystal structure of mouse DNMT1 in complex with acg DNA
Analyse Crystal structure of mouse DNMT1 in complex with acg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8V
- Type
- protein + DNA
- Length
- 1,704 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; Acg DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*…
- EC
- 2.1.1.37
- UniProt
- P13864
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 831 | 20% helix, 27% strand | P13864 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 825 | 21% helix, 27% strand | P13864 |
| C, E | Acg DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3') | dna | 12 | — | — |
| D, F | Acg DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D, B, F
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.83 | 0.85 | 100 | empty |
| 2 | 683 | 0.79 | 0.84 | 76 | empty |
| 3 | 611 | 0.71 | 0.79 | 54 | empty |
| 4 | 601 | 0.71 | 0.79 | 47 | empty |
| 5 | 211 | 0.70 | 0.88 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1290 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1136 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–F · 1133 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 929 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–E · 911 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6W8V · Crystal structure of mouse DNMT1 in complex with ACG DNA · the same entry in another collection · chain F against F, TM-score 1.00
- P13864 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P13864) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P13864
- Elsewhere: RCSB PDB 6W8V · PDBe 6W8V · UniProt P13864
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