MolNFT v1 · #180588 · protein + DNA
Crystal structure of the DRM2-cct DNA complex
7L4M · DNA (cytosine-5)-methyltransferase DRM2: “Crystal structure of the DRM2-cct DNA complex”. X-ray diffraction, 2 ligands (SAH, DT), 20 pockets (best druggability 0.76). MolNFT v1 #180588 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L4M
- Type
- protein + DNA
- Length
- 770 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, DT
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 35% 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 | 35% helix, 15% strand | Q9M548 |
| C, E | DNA (5'- D(*TP*AP*AP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3') | dna | 18 | — | — |
| D | DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49) P*CP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 18 | — | — |
| G | DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49) P*CP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 16 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, D, A, G
- DT · Thymidine-5'-monophosphate · ligand · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.76 | 0.95 | 27 | empty |
| 2 | 619 | 0.71 | 0.79 | 54 | empty |
| 3 | 73 | 0.71 | 0.96 | 19 | empty |
| 4 | 442 | 0.70 | 0.81 | 49 | SAH |
| 5 | 265 | 0.67 | 0.83 | 36 | SAH |
Interfaces
7 interfaces between chains.
- A–G · 999 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 940 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–A · 880 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 749 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- B–C · 747 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 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 7L4M · PDBe 7L4M · UniProt Q9M548
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