MolNFT v1 · #154125 · protein
DNA methyltransferase in complex with sinefungin
6K0W · Adenine specific DNA methyltransferase (mod): “DNA methyltransferase in complex with sinefungin”. X-ray diffraction, 1 ligand (SFG), 20 pockets (best druggability 0.76). MolNFT v1 #154125 on GenesisL1: 3D structure, binding sites…
- PDB
- 6K0W
- Type
- protein
- Length
- 1,895 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine specific DNA methyltransferase (mod)
- UniProt
- O25315
- Ligands
- SFG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Adenine specific DNA methyltransferase (mod) | protein | 499 | 35% helix, 20% strand | O25315 |
| A | Adenine specific DNA methyltransferase (mod) | protein | 528 | 33% helix, 19% strand | O25315 |
| C | Adenine specific DNA methyltransferase (mod) | protein | 433 | 37% helix, 21% strand | O25315 |
| D | Adenine specific DNA methyltransferase (mod) | protein | 435 | 39% helix, 17% strand | O25315 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.97 | 18 | empty |
| 2 | 80 | 0.75 | 0.98 | 19 | empty |
| 3 | 983 | 0.73 | 0.77 | 88 | SFG |
| 4 | 933 | 0.73 | 0.77 | 89 | SFG |
| 5 | 912 | 0.73 | 0.77 | 80 | SFG |
Interfaces
3 interfaces between chains.
- B–D · 2325 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 33 hydrogen bonds · protein-protein
- B–A · 197 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6K0W · DNA methyltransferase in complex with sinefungin · the same entry in another collection · chain C against C, TM-score 1.00
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 O25315
- Elsewhere: RCSB PDB 6K0W · PDBe 6K0W · UniProt O25315
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