MolNFT v1 · #128467 · protein
Human DNMT3B pwwp domain in complex with ethambutol
5NR3 · DNA (cytosine-5)-methyltransferase 3B: “Human DNMT3B pwwp domain in complex with ethambutol”. X-ray diffraction, 2 ligands (95E, SO4), 1 pocket (best druggability 0.62). MolNFT v1 #128467 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NR3
- 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
- 95E, SO4
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 131 | 40% helix, 18% strand | Q9UBC3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.62 | 0.77 | 56 | 95E, SO4 |
Interfaces
1 interface between chains.
- A–B · 551 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NR3 · Human DNMT3B PWWP domain in complex with ethambutol · 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 5NR3 · PDBe 5NR3 · UniProt Q9UBC3
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