Research workbench
Crystal structure of mouse DNMT1(731-1602) in the free state
Analyse Crystal structure of mouse DNMT1(731-1602) in the free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PT9
- Type
- protein
- Length
- 824 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- UniProt
- P13864
- Ligands
- SAH, ZN
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 824 | 23% helix, 27% strand | P13864 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.71 | 0.78 | 57 | empty |
| 2 | 337 | 0.62 | 0.78 | 45 | SAH |
| 3 | 315 | 0.59 | 0.77 | 45 | empty |
| 4 | 124 | 0.44 | 0.77 | 21 | empty |
| 5 | 72 | 0.39 | 0.78 | 18 | empty |
Compared structures
- 3PT9 · Crystal structure of mouse DNMT1(731-1602) in the free state · the same entry in another collection · chain A against A, 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 0.99
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 P13864
- Elsewhere: RCSB PDB 3PT9 · PDBe 3PT9 · UniProt P13864
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