Research workbench
Complex of escherichia COLI DNA adenine methyltransferase (dam) with adomet and a 5-bp non-canonical site (gttta )
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
- 4RTR
- Type
- protein + DNA
- Length
- 267 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA adenine methylase; DNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3'); DNA…
- UniProt
- H0Q7C9
- Ligands
- SAM
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA adenine methylase | protein | 244 | 43% helix, 17% strand | H0Q7C9 |
| F | DNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3') | dna | 11 | — | — |
| G | DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.55 | 0.76 | 35 | SAM |
| 2 | 68 | 0.31 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- F–G · 471 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–G · 300 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 21 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4RTR · 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 4RTR · PDBe 4RTR · UniProt H0Q7C9
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