MolNFT v1 · #154517 · protein
Crystal structure of human DNMT3B-DNMT3L complex (II)
6KDP · DNA (cytosine-5)-methyltransferase 3B: “Crystal structure of human DNMT3B-DNMT3L complex (II)”. X-ray diffraction, 1 ligand (SAH), 8 pockets (best druggability 0.67). MolNFT v1 #154517 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KDP
- Type
- protein
- Length
- 942 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
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 277 | 32% helix, 17% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 191 | 31% helix, 19% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 197 | 33% helix, 18% strand | Q9UJW3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
- FMT · Formic acid · additive · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.67 | 0.83 | 41 | SAH |
| 2 | 269 | 0.63 | 0.81 | 42 | SAH |
| 3 | 366 | 0.58 | 0.75 | 38 | empty |
| 4 | 84 | 0.55 | 0.86 | 16 | empty |
| 5 | 293 | 0.52 | 0.74 | 38 | empty |
Interfaces
3 interfaces between chains.
- C–D · 936 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 915 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6KDP · Crystal structure of human DNMT3B-DNMT3L complex (II) · the same entry in another collection · chain D against D, 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 D 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 0.98
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
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6KDP · PDBe 6KDP · UniProt Q9UBC3 · UniProt Q9UJW3
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