Research workbench
Structure of DNMT1 rfts domain in complex with ubiquitin
Analyse Structure of DNMT1 rfts domain in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YDR
- Type
- protein
- Length
- 398 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B; DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- UniProt
- J3QS39, P26358
- Ligands
- ZN, PO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | J3QS39 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 250 | 32% helix, 18% strand | P26358 |
| D | Polyubiquitin-B | protein | 73 | 26% helix, 38% strand | J3QS39 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.69 | 0.88 | 31 | empty |
| 2 | 420 | 0.69 | 0.80 | 37 | empty |
| 3 | 157 | 0.50 | 0.78 | 29 | empty |
| 4 | 57 | 0.32 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YDR · Structure of DNMT1 RFTS domain in complex with ubiquitin · 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 B against A, TM-score 0.74
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 J3QS39
- Every structure of UniProt P26358
- Elsewhere: RCSB PDB 5YDR · PDBe 5YDR · UniProt J3QS39 · UniProt P26358
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