MolNFT v1 · #85006 · DNA

Molecular and crystal structure of D(CGCGMO6AATCCGCG): the watson-crick type N6-METHOXYADENOSINE/CYTIDINE base-pairs in B-DNA

456D · DNA (5'-D(*CP*GP*CP*GP*(A47) P*AP*TP*CP*CP*GP*CP*G)-3'): “Molecular and crystal structure of D(CGCGMO6AATCCGCG): the watson-crick type N6-METHOXYADENOSINE/CYTIDINE…”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability…

PDB: 456D
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*GP*(A47) P*AP*TP*CP*CP*GP*CP*G)-3')
Ligands: MG
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPGPCPGP(A47) PAPTPCPCPGPCPG)-3')	dna	12	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.28	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 591 Å² buried · 51 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

456D · Molecular and crystal structure of D(CGCGMO6AATCCGCG): the watson-crick type… · 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 456D · PDBe 456D

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