MolNFT v1 · #180589 · protein + DNA
Crystal structure of the DRM2 (C397R)-ccg DNA complex
7L4N · DNA (cytosine-5)-methyltransferase DRM2: “Crystal structure of the DRM2 (C397R)-ccg DNA complex”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.71). MolNFT v1 #180589 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L4N
- 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
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase DRM2 (EC 2.1.1.37) | protein | 352 | 37% helix, 15% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.71 | 0.80 | 57 | SAH |
| 2 | 373 | 0.65 | 0.80 | 40 | empty |
| 3 | 97 | 0.51 | 0.83 | 19 | empty |
| 4 | 89 | 0.38 | 0.77 | 13 | empty |
| 5 | 69 | 0.35 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1042 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 830 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 759 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7L4N · Crystal structure of the DRM2 (C397R)-CCG DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9M548 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase DRM2 (Q9M548) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 7L4N · PDBe 7L4N · UniProt Q9M548
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