MolNFT v1 · #138827 · protein
Crystal structure of DNMT1 rfts domain in complex with K18/K23 mono- ubiquitylated histone H3
5WVO · Ubiquitin: “Crystal structure of DNMT1 rfts domain in complex with K18/K23 mono- ubiquitylated histone H3”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #138827 on GenesisL1: 3D structure, binding…
- PDB
- 5WVO
- Type
- protein
- Length
- 403 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; DNA (cytosine-5)-methyltransferase 1; Histone H3.1
- EC
- 2.1.1.37
- UniProt
- P62979, P26358, P68431
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin | protein | 76 | 25% helix, 36% strand | P62979 |
| C | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 232 | 30% helix, 19% strand | P26358 |
| D | Histone H3.1 | protein | 19 | 0% helix, 37% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.68 | 0.89 | 30 | empty |
| 2 | 318 | 0.63 | 0.80 | 51 | empty |
| 3 | 239 | 0.59 | 0.79 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1110 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1000 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 970 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 452 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WVO · Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone… · 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 C against A, TM-score 0.75
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 P62979
- Every structure of UniProt P26358
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 5WVO · PDBe 5WVO · UniProt P62979 · UniProt P26358 · UniProt P68431
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