Research workbench
Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTCTA)
Analyse Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RTS
- Type
- protein + DNA
- Length
- 266 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.49
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- DNA adenine methylase; DNA (5'-D(*AP*CP*TP*TP*AP*GP*AP*CP*TP*TP*AP*G)-3'); DNA…
- UniProt
- H0Q7C9
- Ligands
- SAM
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.49 · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA adenine methylase | protein | 243 | 43% helix, 17% strand | H0Q7C9 |
| F | DNA (5'-D(*AP*CP*TP*TP*AP*GP*AP*CP*TP*TP*AP*G)-3') | dna | 11 | — | — |
| G | DNA (5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*TP*AP*AP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.59 | 0.78 | 43 | SAM |
Interfaces
3 interfaces between chains.
- F–G · 495 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–G · 323 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 23 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4RTS · Complex of escherichia COLI DNA adenine methyltransferase (dam) with adomet and a 5-bp… · the same entry in another collection · chain A against A, 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 H0Q7C9
- Elsewhere: RCSB PDB 4RTS · PDBe 4RTS · UniProt H0Q7C9
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