MolNFT v1 · #107354 · protein
Crystal structure of DNMT3A-DNMT3L in complex with histone H3
4U7T · DNA (cytosine-5)-methyltransferase 3A: “Crystal structure of DNMT3A-DNMT3L in complex with histone H3”. X-ray diffraction, 2 ligands (SAH, ZN), 17 pockets (best druggability 0.72). MolNFT v1 #107354 on GenesisL1: 3D structure…
- PDB
- 4U7T
- Type
- protein
- Length
- 1,233 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A; DNA (cytosine-5)-methyltransferase 3-like; Peptide…
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3, P84243
- Ligands
- SAH, ZN
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 417 | 32% helix, 17% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 187 | 32% helix, 13% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 418 | 31% helix, 17% strand | Q9Y6K1 |
| D | DNA (cytosine-5)-methyltransferase 3-like | protein | 191 | 34% helix, 14% strand | Q9UJW3 |
| F, G | Peptide from histone H3.3 | protein | 10 | 0% helix, 30% strand | P84243 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.72 | 0.95 | 22 | empty |
| 2 | 691 | 0.71 | 0.78 | 74 | empty |
| 3 | 700 | 0.70 | 0.77 | 84 | empty |
| 4 | 415 | 0.67 | 0.80 | 58 | SAH |
| 5 | 285 | 0.67 | 0.83 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 967 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 959 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 716 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 654 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4U7T · Crystal structure of DNMT3A-DNMT3L in complex with histone H3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6K1 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) · 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
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain G against A, TM-score 0.40
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 Q9Y6K1
- Every structure of UniProt Q9UJW3
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 4U7T · PDBe 4U7T · UniProt Q9Y6K1 · UniProt Q9UJW3 · UniProt P84243
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