Research workbench
Structural basis of the recognition of H3K36ME3 by DNMT3B pwwp domain
Analyse Structural basis of the recognition of H3K36ME3 by DNMT3B pwwp domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIU
- Type
- protein
- Length
- 262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3B; Histone H3.2
- EC
- 2.1.1.37
- UniProt
- Q9UBC3
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 127 | 34% helix, 19% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 121 | 32% helix, 19% strand | Q9UBC3 |
| C, D | Histone H3.2 | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B, C
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 | 423 | 0.68 | 0.80 | 42 | empty |
| 2 | 66 | 0.39 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 574 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 463 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5CIU · Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain · 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 0.98
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 5CIU · PDBe 5CIU · UniProt Q9UBC3
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