Research workbench
CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor MC4756 (Compound 178)
Analyse CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CY0
- Type
- protein + DNA
- Length
- 1,717 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Clostridioides difficile; SYNTHETIC CONSTRUCT
- Molecule
- Site-specific DNA-methyltransferase (adenine-specific); DNA…
- EC
- 2.1.1.72
- UniProt
- A0A031WG99
- Ligands
- Q9W, K
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.65 · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 545 | 40% helix, 20% strand | A0A031WG99 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 550 | 40% helix, 20% strand | A0A031WG99 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 538 | 41% helix, 20% strand | A0A031WG99 |
| E, G, I | DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3') | dna | 14 | — | — |
| D, F, H | DNA (5'-D(*AP*TP*GP*GP*GP*AP*CP*TP*TP*TP*TP*TP*GP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- Q9W · N-(4-phenylbutyl)adenosine · ligand · 3 copies · chains A, D, B, F, C, H
- K · Potassium ion · metal · 7 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, F, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.69 | 0.74 | 84 | EDO |
| 2 | 412 | 0.67 | 0.80 | 45 | K, EDO |
| 3 | 320 | 0.66 | 0.81 | 39 | empty |
| 4 | 334 | 0.65 | 0.80 | 43 | K |
| 5 | 357 | 0.63 | 0.79 | 40 | K |
Interfaces
18 interfaces between chains.
- C–H · 1328 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–F · 1305 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–D · 1293 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–E · 1161 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–G · 1133 Ų buried · 18 hydrogen bonds · protein-nucleic
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 A0A031WG99
- Elsewhere: RCSB PDB 8CY0 · PDBe 8CY0 · UniProt A0A031WG99
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