MolNFT v1 · #138899 · protein
Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant)
5WY1 · DNA (cytosine-5)-methyltransferase 1: “Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant)”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.74). MolNFT v1 #138899 on GenesisL1: 3D structure, binding…
- PDB
- 5WY1
- Type
- protein
- Length
- 1,140 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
- ZN
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 1140 | 26% helix, 23% strand | P13864 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.74 | 0.80 | 61 | empty |
| 2 | 497 | 0.71 | 0.81 | 58 | empty |
| 3 | 410 | 0.70 | 0.81 | 46 | empty |
| 4 | 452 | 0.66 | 0.78 | 42 | empty |
| 5 | 301 | 0.55 | 0.75 | 48 | empty |
Compared structures
- 5WY1 · Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant) · 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 0.97
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 5WY1 · PDBe 5WY1 · UniProt P13864
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