MolNFT v1 · #154513 · protein
Crystal structure of human DNMT3B-DNMT3L complex (I)
6KDL · DNA (cytosine-5)-methyltransferase 3B: “Crystal structure of human DNMT3B-DNMT3L complex (I)”. X-ray diffraction, 1 ligand (SAH), 16 pockets (best druggability 0.65). MolNFT v1 #154513 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KDL
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3B; DNA (cytosine-5)-methyltransferase 3-like
- EC
- 2.1.1.37
- UniProt
- Q9UBC3, Q9UJW3
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 277 | 31% helix, 18% strand | Q9UBC3 |
| B, C | DNA (cytosine-5)-methyltransferase 3-like | protein | 179 | 33% helix, 13% strand | Q9UJW3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.65 | 0.80 | 45 | SAH |
| 2 | 315 | 0.64 | 0.80 | 47 | SAH |
| 3 | 71 | 0.60 | 0.90 | 19 | empty |
| 4 | 397 | 0.59 | 0.76 | 40 | empty |
| 5 | 65 | 0.57 | 0.89 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 960 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 953 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 936 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6KDL · Crystal structure of human DNMT3B-DNMT3L complex (I) · the same entry in another collection · chain C against C, 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
- Q9UJW3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3-like (Q9UJW3) · a predicted model of the same protein · chain B against A, TM-score 0.97
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
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6KDL · PDBe 6KDL · UniProt Q9UBC3 · UniProt Q9UJW3
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