MolNFT v1 · #75535 · protein + DNA
Crystal structure of mouse DNMT1(650-1602) in complex with DNA
3PT6 · DNA (cytosine-5)-methyltransferase 1: “Crystal structure of mouse DNMT1(650-1602) in complex with DNA”. X-ray diffraction, 2 ligands (SAH, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #75535 on GenesisL1: 3D structure…
- PDB
- 3PT6
- Type
- protein + DNA
- Length
- 1,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; DNA (5'…
- EC
- 2.1.1.37
- UniProt
- P13864
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 914 | 21% helix, 25% strand | P13864 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 915 | 22% helix, 26% strand | P13864 |
| C, D | DNA (5'- D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') | dna | 19 | — | — |
| I, J | DNA (5'- D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.82 | 0.84 | 94 | SAH |
| 2 | 1001 | 0.82 | 0.83 | 116 | SAH |
| 3 | 675 | 0.72 | 0.78 | 59 | empty |
| 4 | 327 | 0.71 | 0.84 | 43 | empty |
| 5 | 450 | 0.69 | 0.80 | 40 | empty |
Interfaces
11 interfaces between chains.
- C–I · 885 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- D–J · 865 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–B · 739 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 675 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 666 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3PT6 · Crystal structure of mouse DNMT1(650-1602) in complex with DNA · the same entry in another collection · chain J against J, 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 A against A, TM-score 0.96
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 3PT6 · PDBe 3PT6 · UniProt P13864
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