MolNFT v1 · #183820 · protein
Crystal structure of add domain of the human DNMT3B methyltransferase
7O45 · Isoform 6 of DNA (cytosine-5)-methyltransferase 3B: “Crystal structure of add domain of the human DNMT3B methyltransferase”. X-ray diffraction, 2 ligands (ZN, BR), 9 pockets (best druggability 0.76). MolNFT v1 #183820 on GenesisL1…
- PDB
- 7O45
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 6 of DNA (cytosine-5)-methyltransferase 3B
- EC
- 2.1.1.37
- UniProt
- Q9UBC3
- Ligands
- ZN, BR
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Isoform 6 of DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 141 | 31% helix, 16% strand | Q9UBC3 |
| D | Isoform 6 of DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 84 | 24% helix, 10% strand | Q9UBC3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
- BR · Bromide ion · ion · 3 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 16 | empty |
| 2 | 63 | 0.75 | 0.99 | 16 | empty |
| 3 | 59 | 0.74 | 0.99 | 16 | empty |
| 4 | 678 | 0.70 | 0.77 | 63 | BR |
| 5 | 152 | 0.61 | 0.84 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 777 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 699 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7O45 · Crystal structure of ADD domain of the human DNMT3B methyltransferase · 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 A against A, TM-score 0.94
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 7O45 · PDBe 7O45 · UniProt Q9UBC3
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