Research workbench
The crystal structure of human DNMT1(351-1600)
Analyse The crystal structure of human DNMT1(351-1600) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WXX
- Type
- protein
- Length
- 2,347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 1169 | 24% helix, 22% strand | P26358 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 1178 | 24% helix, 22% strand | P26358 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.82 | 0.83 | 119 | empty |
| 2 | 1013 | 0.80 | 0.81 | 108 | SAH |
| 3 | 1136 | 0.78 | 0.80 | 116 | empty |
| 4 | 716 | 0.76 | 0.81 | 77 | SAH |
| 5 | 930 | 0.75 | 0.78 | 81 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- P26358 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P26358) · 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 P26358
- Elsewhere: RCSB PDB 4WXX · PDBe 4WXX · UniProt P26358
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