Research workbench
Crystal structure of mouse DNMT1 in complex with ccg DNA
Analyse Crystal structure of mouse DNMT1 in complex with ccg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8W
- Type
- protein + DNA
- Length
- 1,702 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; Ccg DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*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, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 828 | 21% helix, 26% strand | P13864 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 826 | 21% helix, 26% strand | P13864 |
| C, E | Ccg DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') | dna | 12 | — | — |
| D, F | Ccg DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.83 | 0.85 | 91 | empty |
| 2 | 692 | 0.79 | 0.84 | 76 | empty |
| 3 | 679 | 0.72 | 0.78 | 52 | empty |
| 4 | 630 | 0.70 | 0.78 | 52 | empty |
| 5 | 255 | 0.69 | 0.85 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1401 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1135 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–F · 1098 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 960 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–E · 949 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6W8W · Crystal structure of mouse DNMT1 in complex with CCG DNA · the same entry in another collection · chain B against B, 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 6W8W · PDBe 6W8W · UniProt P13864
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