MolNFT v1 · #180581 · protein + DNA
Crystal structure of the DRM2-cat DNA complex
7L4F · DNA (cytosine-5)-methyltransferase DRM2: “Crystal structure of the DRM2-cat DNA complex”. X-ray diffraction, 2 ligands (SAH, DA), 15 pockets (best druggability 0.75). MolNFT v1 #180581 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L4F
- Type
- protein + DNA
- Length
- 771 residues
- Chains
- 6
- 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, DA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | DNA (cytosine-5)-methyltransferase DRM2 (EC 2.1.1.37) | protein | 350 | 37% helix, 15% strand | Q9M548 |
| C, E | DNA (5'- D(*TP*AP*AP*AP*GP*GP*AP*TP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49) P*AP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 18 | — | — |
| G | DNA (5'-D(*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49) P*AP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, D, A, G
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.75 | 0.97 | 21 | empty |
| 2 | 524 | 0.73 | 0.81 | 64 | SAH |
| 3 | 503 | 0.72 | 0.81 | 50 | empty |
| 4 | 186 | 0.66 | 0.85 | 36 | empty |
| 5 | 253 | 0.65 | 0.82 | 35 | SAH |
Interfaces
7 interfaces between chains.
- A–G · 959 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 953 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 900 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 733 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- C–D · 731 Ų buried · 76 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent (nucleotide modification, covalent ligand).
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 7L4F · PDBe 7L4F · UniProt Q9M548
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