Research workbench
Crystal structure of the DRM2-ctg DNA complex
Analyse Crystal structure of the DRM2-ctg DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4H
- Type
- protein + DNA
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase DRM2; DNA (5'…
- EC
- 2.1.1.37
- UniProt
- Q9M548
- Ligands
- SAH, IOD
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase DRM2 (EC 2.1.1.37) | protein | 352 | 37% helix, 14% strand | Q9M548 |
| B | DNA (5'- D(*TP*AP*AP*AP*TP*TP*CP*AP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3') | dna | 18 | — | — |
| C | DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49) P*TP*GP*AP*AP*TP*TP*TP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- IOD · Iodide ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.66 | 0.80 | 37 | empty |
| 2 | 297 | 0.63 | 0.80 | 36 | SAH, IOD |
| 3 | 232 | 0.58 | 0.80 | 26 | empty |
| 4 | 93 | 0.37 | 0.76 | 12 | empty |
| 5 | 75 | 0.36 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1016 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 806 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 747 Ų buried · 67 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 Q9M548
- Elsewhere: RCSB PDB 7L4H · PDBe 7L4H · UniProt Q9M548
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.