Research workbench
Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor GSK3830052
Analyse Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna and inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X9J
- 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 (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3…
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- X52, ZN
- Pockets
- 11 · 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 (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)- 3') | dna | 12 | — | — |
Ligands and binding sites
- X52 · N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino) ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide · ligand · chains A, C, D
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.83 | 0.85 | 107 | EDO, X52 |
| 2 | 751 | 0.73 | 0.79 | 76 | EDO |
| 3 | 122 | 0.54 | 0.83 | 28 | empty |
| 4 | 216 | 0.53 | 0.78 | 28 | empty |
| 5 | 96 | 0.53 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 630 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 553 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 531 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6X9J · Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 · 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 6X9J · PDBe 6X9J · UniProt P26358
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