MolNFT v1 · #169360 · protein + DNA
Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna
6X9I · DNA (cytosine-5)-methyltransferase 1: “Human DNMT1(729-1600) bound to zebularine-containing 12MER dsdna”. X-ray diffraction, 2 ligands (SAH, ZN), 13 pockets (best druggability 0.82). MolNFT v1 #169360 on GenesisL1: 3D structure…
- PDB
- 6X9I
- Type
- protein + DNA
- Length
- 839 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
- SAH, ZN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 815 | 22% helix, 27% 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
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.82 | 0.83 | 117 | SAH |
| 2 | 814 | 0.73 | 0.78 | 79 | GOL |
| 3 | 254 | 0.61 | 0.81 | 31 | empty |
| 4 | 197 | 0.55 | 0.79 | 29 | empty |
| 5 | 95 | 0.47 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1086 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 910 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 508 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6X9I · Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA · 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 6X9I · PDBe 6X9I · UniProt P26358
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