Research workbench
Crystal structure of the DRM2-ctt DNA complex
Analyse Crystal structure of the DRM2-ctt DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4C
- Type
- protein + DNA
- Length
- 389 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
- 6 · best druggability 0.70
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 | 353 | 37% helix, 14% strand | Q9M548 |
| B | DNA (5'- D(*TP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3') | dna | 18 | — | — |
| C | DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49) P*TP*TP*AP*AP*TP*TP*TP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.70 | 0.80 | 57 | SAH |
| 2 | 268 | 0.60 | 0.80 | 33 | empty |
| 3 | 53 | 0.42 | 0.83 | 17 | empty |
| 4 | 85 | 0.36 | 0.75 | 18 | empty |
| 5 | 87 | 0.33 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 950 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 860 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 751 Ų buried · 62 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 7L4C · PDBe 7L4C · UniProt Q9M548
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