Research workbench
Complex of escherichia COLI DNA adenine methyltransferase (dam) with sinefungin and with DNA containing distal pap regulon sequence
Analyse Complex of escherichia COLI DNA adenine methyltransferase (dam) with sinefungin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RTL
- Type
- protein + DNA
- Length
- 276 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA adenine methylase; DNA (5'-D(*TP*CP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3'); DNA…
- UniProt
- H0Q7C9
- Ligands
- SFG
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA adenine methylase | protein | 254 | 42% helix, 19% strand | H0Q7C9 |
| F | DNA (5'-D(*TP*CP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3') | dna | 11 | — | — |
| G | DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- SFG · Sinefungin · 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 | 364 | 0.62 | 0.78 | 45 | SFG |
| 2 | 53 | 0.42 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- F–G · 435 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–G · 302 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–F · 16 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4RTL · Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with Sinefungin and with… · 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 4RTL · PDBe 4RTL · UniProt H0Q7C9
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