MolNFT v1 · #106250 · protein + DNA

Complex of escherichia COLI DNA adenine methyltransferase (dam) with sinefungin and with DNA containing proximal pap regulon sequence

4RTO · DNA adenine methylase: “Complex of escherichia COLI DNA adenine methyltransferase (dam) with sinefungin and with DNA containing…”. X-ray diffraction, 1 ligand (SFG), 2 pockets (best druggability 0.55). MolNFT v1 #106250 on…

PDB: 4RTO
Type: protein + DNA
Length: 271 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA adenine methylase; DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3'); DNA…
UniProt: H0Q7C9
Ligands: SFG
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA adenine methylase	protein	249	42% helix, 19% strand	H0Q7C9
F	DNA (5'-D(TPTPTPAPAPAPGPAPTPCP*G)-3')	dna	11	—	—
G	DNA (5'-D(APCPGPAPTPCPTPTPTPAP*A)-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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.55	0.78	34	SFG
2	70	0.39	0.79	24	empty

Interfaces

3 interfaces between chains.

F–G · 441 Å² buried · 40 hydrogen bonds · nucleic-nucleic
A–F · 311 Å² buried · 8 hydrogen bonds · protein-nucleic
A–G · 33 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

4RTO · 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 4RTO · PDBe 4RTO · UniProt H0Q7C9

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