MolNFT v2 · #5577 · DNA

Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin

1EM0 · DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3'): “Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin”. X-ray diffraction at 0.9, 2 ligands (PNI, MG). MolNFT v2 #5577 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1EM0
Type: DNA
Length: 24 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 0.9
Molecule: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
Ligands: PNI, MG

Structure

x-ray diffraction · resolution 0.9 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D((CBR)PCPTPAPGPG)-3')	dna	6	—	—

Ligands and binding sites

PNI · Tetra[n-methyl-pyridyl] porphyrin-nickel · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

6 interfaces between chains.

A–B · 283 Å² buried · 19 hydrogen bonds · nucleic-nucleic
C–D · 280 Å² buried · 19 hydrogen bonds · nucleic-nucleic
A–D · 112 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–C · 111 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–C · 36 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

1EM0 · Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin · 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
Elsewhere: RCSB PDB 1EM0 · PDBe 1EM0

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