Research workbench
Structure of human DNMT1 (601-1600) in complex with sinefungin
Analyse Structure of human DNMT1 (601-1600) in complex with sinefungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SWR
- Type
- protein
- Length
- 965 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
- P26358
- Ligands
- SFG, ZN, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 965 | 23% helix, 22% strand | P26358 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 25 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.75 | 0.81 | 53 | EDO |
| 2 | 685 | 0.74 | 0.80 | 66 | SFG, EDO |
| 3 | 840 | 0.69 | 0.75 | 74 | EDO |
| 4 | 330 | 0.64 | 0.80 | 30 | EDO |
| 5 | 287 | 0.60 | 0.79 | 42 | SO4 |
Compared structures
- 3SWR · Structure of human DNMT1 (601-1600) in complex with Sinefungin · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.93
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 3SWR · PDBe 3SWR · UniProt P26358
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