MolNFT v1 · #85011 · DNA

A "hydrat-ion spine" in a B-DNA minor groove

461D · DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF) P*TP*CP*GP*CP*G)-3'): “A "hydrat-ion spine" in a B-DNA minor groove”. X-ray diffraction, 2 ligands (MG, RB). MolNFT v1 #85011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 461D
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*AP*AP*(TAF) P*TP*CP*GP*CP*G)-3')
Ligands: MG, RB

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPGPCPGPAPAP(TAF) PTPCPGPCPG)-3')	dna	12	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
RB · Rubidium ion · metal · chains A, B

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

Interfaces

1 interface between chains.

A–B · 570 Å² buried · 51 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

461D · A "hydrat-ion spine" in a B-DNA minor groove · 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 461D · PDBe 461D

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