Research workbench
Crystal structure of human DNMT1(646-1600) in complex with DNA
Analyse Crystal structure of human DNMT1(646-1600) in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PTA
- Type
- protein + DNA
- Length
- 942 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; DNA (5'…
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- SAH, ZN
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 904 | 21% helix, 23% strand | P26358 |
| B | DNA (5'- D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') | dna | 19 | — | — |
| C | DNA (5'- D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.83 | 0.85 | 92 | SAH |
| 2 | 711 | 0.76 | 0.81 | 65 | empty |
| 3 | 596 | 0.71 | 0.79 | 55 | empty |
| 4 | 310 | 0.61 | 0.79 | 30 | empty |
| 5 | 162 | 0.51 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 850 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–B · 510 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 328 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3PTA · Crystal structure of human DNMT1(646-1600) in complex with DNA · the same entry in another collection · chain C against C, 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 0.95
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 3PTA · PDBe 3PTA · UniProt P26358
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