MolNFT v1 · #162251 · protein
Human DNMT3B pwwp domain in complex with triisopropanolamine
6R3E · DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)…: “Human DNMT3B pwwp domain in complex with triisopropanolamine”. X-ray diffraction, 2 ligands (96H, SO4), 3 pockets (best druggability 0.58). MolNFT v1 #162251 on GenesisL1: 3D…
- PDB
- 6R3E
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)- methyltransferase 3B
- EC
- 2.1.1.37
- UniProt
- Q9UBC3
- Ligands
- 96H, SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)- methyltransferase 3B (EC 2.1.1.37) | protein | 133 | 38% helix, 20% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)- methyltransferase 3B (EC 2.1.1.37) | protein | 131 | 36% helix, 18% strand | Q9UBC3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.58 | 0.77 | 39 | SO4 |
| 2 | 57 | 0.38 | 0.79 | 14 | empty |
| 3 | 51 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6R3E · Human DNMT3B PWWP domain in complex with triisopropanolamine · the same entry in another collection · chain A against A, 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 A 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 6R3E · PDBe 6R3E · UniProt Q9UBC3
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