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MolNFT v1 · #106252 · protein + DNA

Complex of escherichia COLI DNA adenine methyltransferase (dam) with adohcy and a 5-bp non-canonical site (gttta )

4RTQ · DNA adenine methylase: “Complex of escherichia COLI DNA adenine methyltransferase (dam) with adohcy and a 5-bp non-canonical site…”. X-ray diffraction, 1 ligand (SAH), 1 pocket (best druggability 0.54). MolNFT v1 #106252 on…

PDB
4RTQ
Type
protein + DNA
Length
269 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
SAH
Pockets
1 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA adenine methylaseprotein24644% helix, 17% strandH0Q7C9
FDNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')dna11——
GDNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*G)-3')dna12——

Ligands and binding sites

  • SAH · S-adenosyl-L-homocysteine · ligand · chains A
  • EDO · 1,2-ethanediol · additive · chains F, G

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12450.540.7636SAH

Interfaces

3 interfaces between chains.

  • F–G · 471 Ų buried · 40 hydrogen bonds · nucleic-nucleic
  • A–G · 297 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–F · 20 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 4RTQ · Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and a 5-bp… · the same entry in another collection · chain A against A, TM-score 1.00

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