MolNFT v1 · #128584 · protein
Human DNMT3B pwwp domain in complex with N1-(2-hydroxyethyl)-2-methyl- 1,2-propanediamine
5NV7 · DNA (cytosine-5)-methyltransferase 3B: “Human DNMT3B pwwp domain in complex with N1-(2-hydroxyethyl)-2-methyl- 1,2-propanediamine”. X-ray diffraction, 2 ligands (9AK, SO4), 2 pockets (best druggability 0.63). MolNFT v1 #128584 on…
- PDB
- 5NV7
- Type
- protein
- Length
- 262 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
- 9AK, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 132 | 39% helix, 18% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 130 | 38% helix, 18% strand | Q9UBC3 |
Ligands and binding sites
- 9AK · N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
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 | 409 | 0.63 | 0.77 | 46 | SO4 |
| 2 | 52 | 0.33 | 0.77 | 13 | 9AK |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NV7 · Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine · 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 B 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 5NV7 · PDBe 5NV7 · UniProt Q9UBC3
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