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Crystal structure of the DRM2-ccg DNA complex
Analyse Crystal structure of the DRM2-ccg DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4K
- 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
- Pockets
- 8 · best druggability 0.73
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*GP*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*CP*GP*AP*AP*TP*TP*TP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- GOL · Glycerol · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.73 | 0.97 | 22 | empty |
| 2 | 372 | 0.65 | 0.80 | 40 | empty |
| 3 | 273 | 0.63 | 0.81 | 37 | SAH |
| 4 | 271 | 0.59 | 0.79 | 27 | empty |
| 5 | 58 | 0.35 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 978 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 826 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 752 Ų buried · 68 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 7L4K · PDBe 7L4K · UniProt Q9M548
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