MolNFT v1 · #187466 · protein + DNA
Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3852279B
7SFF · DNA (cytosine-5)-methyltransferase 1: “Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3852279B”. X-ray diffraction, 2 ligands (C79, ZN), 10 pockets (best druggability 0.83). MolNFT v1 #187466 on…
- PDB
- 7SFF
- Type
- protein + DNA
- Length
- 866 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; DNA (12-mer)
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- C79, ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 842 | 25% helix, 26% strand | P26358 |
| C | DNA (12-mer) | dna | 12 | — | — |
| D | DNA (12-mer) | dna | 12 | — | — |
Ligands and binding sites
- C79 · (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl) phenyl]acetamide · ligand · chains A, C, D
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- GOL · Glycerol · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.83 | 0.84 | 109 | C79 |
| 2 | 751 | 0.74 | 0.79 | 73 | EDO |
| 3 | 227 | 0.56 | 0.78 | 30 | empty |
| 4 | 111 | 0.52 | 0.82 | 29 | EDO |
| 5 | 89 | 0.51 | 0.83 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 625 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 535 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–D · 420 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7SFF · Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B · 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 0.98
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 7SFF · PDBe 7SFF · UniProt P26358
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