MolNFT v1 · #120270 · protein
The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A
5GUT · DNA (cytosine-5)-methyltransferase 1: “The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A”. X-ray diffraction, 3 ligands (SAH, ZN, SO4), 10 pockets (best druggability 0.72). MolNFT v1 #120270 on GenesisL1: 3D structure…
- PDB
- 5GUT
- Type
- protein
- Length
- 794 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, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 794 | 25% helix, 27% strand | P13864 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.72 | 0.80 | 50 | empty |
| 2 | 247 | 0.59 | 0.79 | 40 | SAH |
| 3 | 164 | 0.50 | 0.78 | 24 | empty |
| 4 | 174 | 0.49 | 0.77 | 32 | empty |
| 5 | 71 | 0.46 | 0.83 | 21 | empty |
Compared structures
- 5GUT · The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A · 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 5GUT · PDBe 5GUT · UniProt P13864
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