Research workbench
Crystal structure of the pwwp domain of human DNA (cytosine-5-)- methyltransferase 3 alpha
Analyse Crystal structure of the pwwp domain of human DNA (cytosine-5-)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LLR
- Type
- protein
- Length
- 670 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 131 | 41% helix, 18% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 132 | 39% helix, 18% strand | Q9Y6K1 |
| C | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 131 | 40% helix, 18% strand | Q9Y6K1 |
| D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 143 | 39% helix, 17% strand | Q9Y6K1 |
| E | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 133 | 42% helix, 20% strand | Q9Y6K1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.72 | 0.76 | 82 | BTB |
| 2 | 238 | 0.65 | 0.83 | 29 | empty |
| 3 | 211 | 0.57 | 0.79 | 26 | empty |
| 4 | 168 | 0.56 | 0.81 | 21 | empty |
| 5 | 152 | 0.55 | 0.81 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–D · 895 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 677 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 570 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 383 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LLR · Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha · the same entry in another collection · chain E against E, 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 0.98
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 Q9Y6K1
- Elsewhere: RCSB PDB 3LLR · PDBe 3LLR · UniProt Q9Y6K1
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