Research workbench

DNA/RNA (5'-R(CP)-D(CPGPGPCPGPCPCPGP)- R(G)-3')

Analyse DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3') in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 100D
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3')
Ligands: SPM
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA/RNA (5'-R(CP)-D(CPGPGPCPGPCPCPGP)- R(G)-3')	dna	10	—	—

Ligands and binding sites

SPM · Spermine · ligand · chains A

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	123	0.35	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 540 Å² buried · 53 hydrogen bonds · nucleic-nucleic

Compared structures

100D · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine… · the same entry in another collection · chain A against A, TM-score 1.00
100D · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine… · 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 100D · PDBe 100D

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