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B-DNA dodecamer CGCGAAT(TLC)CGCG with incorporated [3.3.0]BICYCLO-arabino-thymine-5'-phosphate

Analyse B-DNA dodecamer CGCGAAT(TLC)CGCG with incorporated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EI4
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*(TLC)P*(TLC) P*CP*GP*CP*G)-3')
Ligands: SPM, MG

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

SPM · Spermine · ligand · chains A, B
MG · Magnesium 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 · 571 Å² buried · 49 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1EI4 · B-DNA dodecamer CGCGAAT(TLC)CGCG with incorporated… · 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 1EI4 · PDBe 1EI4

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