Research workbench
Human DNMT3B pwwp domain in complex with 6-dipropylamino-1-hexanol
Analyse Human DNMT3B pwwp domain in complex with 6-dipropylamino-1-hexanol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NRV
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3B
- EC
- 2.1.1.37
- UniProt
- Q9UBC3
- Ligands
- 96K, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 131 | 40% helix, 18% strand | Q9UBC3 |
| A | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 129 | 40% helix, 19% strand | Q9UBC3 |
Ligands and binding sites
- 96K · 6-dipropylamino-1-hexanol · ligand · 2 copies · chains D, A
- SO4 · Sulfate ion · ion · 10 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.64 | 0.77 | 56 | 96K, SO4 |
| 2 | 50 | 0.35 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- D–A · 577 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NRV · Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UBC3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9UBC3
- Elsewhere: RCSB PDB 5NRV · PDBe 5NRV · UniProt Q9UBC3
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