MolNFT v1 · #76429 · protein
The pwwp domain of human DNA (cytosine-5-)-methyltransferase 3 beta in complex with a bis-tris molecule
3QKJ · DNA cytosine-5 methyltransferase 3 beta isoform 6 variant: “The pwwp domain of human DNA (cytosine-5-)-methyltransferase 3 beta in complex with a bis-tris molecule”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability…
- PDB
- 3QKJ
- Type
- protein
- Length
- 524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
- UniProt
- Q59H79
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cytosine-5 methyltransferase 3 beta isoform 6 variant | protein | 130 | 34% helix, 18% strand | Q59H79 |
| B | DNA cytosine-5 methyltransferase 3 beta isoform 6 variant | protein | 132 | 39% helix, 18% strand | Q59H79 |
| C | DNA cytosine-5 methyltransferase 3 beta isoform 6 variant | protein | 131 | 37% helix, 18% strand | Q59H79 |
| D | DNA cytosine-5 methyltransferase 3 beta isoform 6 variant | protein | 131 | 40% helix, 18% strand | Q59H79 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.59 | 0.77 | 38 | empty |
| 2 | 203 | 0.55 | 0.79 | 30 | SO4 |
| 3 | 203 | 0.51 | 0.76 | 25 | SO4 |
| 4 | 144 | 0.47 | 0.77 | 25 | empty |
| 5 | 64 | 0.39 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 533 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 461 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 379 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3QKJ · The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q59H79
- Elsewhere: RCSB PDB 3QKJ · PDBe 3QKJ · UniProt Q59H79
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