MolNFT v1 · #154504 · protein + DNA
Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing cpgpt site
6KDB · DNA (cytosine-5)-methyltransferase 3B: “Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing cpgpt site”. X-ray diffraction, 1 ligand (SAH), 13 pockets (best druggability 0.74). MolNFT v1 #154504 on GenesisL1: 3D…
- PDB
- 6KDB
- Type
- protein + DNA
- Length
- 988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3B; DNA (cytosine-5)-methyltransferase 3-like; DNA…
- EC
- 2.1.1.37
- UniProt
- Q9UBC3, Q9UJW3
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 284 | 32% helix, 18% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 183 | 34% helix, 16% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 187 | 34% helix, 18% strand | Q9UJW3 |
| E, F | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.74 | 0.78 | 110 | SAH |
| 2 | 209 | 0.66 | 0.85 | 34 | SAH |
| 3 | 371 | 0.58 | 0.75 | 43 | empty |
| 4 | 333 | 0.57 | 0.76 | 36 | empty |
| 5 | 150 | 0.57 | 0.83 | 18 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1123 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- C–D · 957 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 920 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 844 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 6KDB · Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site · the same entry in another collection · chain F against F, 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 6KDB · PDBe 6KDB · UniProt Q9UBC3 · UniProt Q9UJW3
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