MolNFT v1 · #4488 · DNA

A-DNA decamer GCGTA(T23)TACGC with incorporated 2'-methoxy-3'- methylenephosphate-thymidine

1DPL · 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3': “A-DNA decamer GCGTA(T23)TACGC with incorporated 2'-methoxy-3'- methylenephosphate-thymidine”. X-ray diffraction, 2 ligands (SPM, MG), 1 pocket (best druggability 0.30). MolNFT v1 #4488 on…

PDB: 1DPL
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
Ligands: SPM, MG
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GPCPGPTPAP(T23)PAPCPGPC)-3'	dna	10	—	—

Ligands and binding sites

SPM · Spermine · ligand · 2 copies · chains B
MG · Magnesium ion · metal · 2 copies · 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	98	0.30	0.72	13	MG

Interfaces

1 interface between chains.

A–B · 483 Å² buried · 37 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1DPL · A-DNA decamer GCGTA(T23)TACGC with incorporated 2'-methoxy-3'-methylenephosphate-thymidine · 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 1DPL · PDBe 1DPL

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