MolNFT v1 · #165869 · protein + DNA
Crystal structure of DNMT3B(K777A)-DNMT3L in complex with cpgpt DNA
6U8W · DNA (cytosine-5)-methyltransferase 3B: “Crystal structure of DNMT3B(K777A)-DNMT3L in complex with cpgpt DNA”. X-ray diffraction, 2 ligands (SAH, MG), 18 pockets (best druggability 0.73). MolNFT v1 #165869 on GenesisL1: 3D structure…
- PDB
- 6U8W
- Type
- protein + DNA
- Length
- 1,004 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; Cpgpt…
- EC
- 2.1.1.37
- UniProt
- Q9UBC3, Q9UJW3
- Ligands
- SAH, MG
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 291 | 33% helix, 17% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 192 | 36% helix, 14% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 180 | 35% helix, 15% strand | Q9UJW3 |
| E, F | Cpgpt DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.73 | 0.77 | 98 | empty |
| 2 | 52 | 0.71 | 0.98 | 16 | empty |
| 3 | 221 | 0.66 | 0.84 | 37 | SAH |
| 4 | 231 | 0.65 | 0.83 | 33 | SAH |
| 5 | 288 | 0.63 | 0.80 | 37 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1178 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–D · 927 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 800 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6U8W · Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA · 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 C 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
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6U8W · PDBe 6U8W · UniProt Q9UBC3 · UniProt Q9UJW3
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