MolNFT v1 · #57115 · DNA

Crystal structures of D(CCGGGCCM5CGG)-orthogonal form

323D · DNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*(5CM)P*GP*G)-3'): “Crystal structures of D(CCGGGCCM5CGG)-orthogonal form”. X-ray diffraction, 1 ligand (SPM). MolNFT v1 #57115 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 323D
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*(5CM)P*GP*G)-3')
Ligands: SPM

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPCPGPGPGPCPCP(5CM)PGPG)-3')	dna	10	—	—

Ligands and binding sites

SPM · Spermine · ligand · 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 · 537 Å² buried · 61 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

323D · Crystal structures of D(CCGGGCCM5CGG)-orthogonal form · 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 323D · PDBe 323D

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