MolNFT v1 · #48501 · protein
DNMT3L recognizes unmethylated histone H3 lysine 4
2PVC · DNA (cytosine-5)-methyltransferase 3-like: “DNMT3L recognizes unmethylated histone H3 lysine 4”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.74). MolNFT v1 #48501 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2PVC
- Type
- protein
- Length
- 1,062 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3-like; Histone H3 peptide
- UniProt
- Q9UJW3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | DNA (cytosine-5)-methyltransferase 3-like | protein | 347 | 31% helix, 14% strand | Q9UJW3 |
| D, E, F | Histone H3 peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.74 | 0.78 | 93 | empty |
| 2 | 52 | 0.70 | 0.97 | 19 | empty |
| 3 | 60 | 0.69 | 0.96 | 22 | empty |
| 4 | 51 | 0.52 | 0.88 | 20 | empty |
| 5 | 115 | 0.51 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 783 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 682 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 496 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 484 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 469 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2PVC · DNMT3L recognizes unmethylated histone H3 lysine 4 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UJW3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3-like (Q9UJW3) · a predicted model of the same protein · chain A 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 Q9UJW3
- Elsewhere: RCSB PDB 2PVC · PDBe 2PVC · UniProt Q9UJW3
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