Research workbench
Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and cofactor SAM
Analyse Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and cofactor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SFG
- Type
- protein + DNA
- Length
- 841 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; DNA strand 1; DNA strand 2
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- SAM, ZN
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 817 | 23% helix, 25% strand | P26358 |
| C | DNA strand 1 | dna | 12 | — | — |
| D | DNA strand 2 | dna | 12 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.77 | 0.85 | 61 | empty |
| 2 | 662 | 0.73 | 0.80 | 58 | GOL, EDO |
| 3 | 363 | 0.70 | 0.82 | 47 | SAM |
| 4 | 255 | 0.61 | 0.80 | 32 | empty |
| 5 | 191 | 0.54 | 0.79 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1100 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 929 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 516 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7SFG · Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM · 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 0.97
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 P26358
- Elsewhere: RCSB PDB 7SFG · PDBe 7SFG · UniProt P26358
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