MolNFT v1 · #3825 · DNA

The structure of a B-DNA decamer with a central T-a step: C- G-a-T-T-a-a-T-C-G

1D49 · DNA (5'-D(*CP*GP*AP*TP*TP*AP*AP*TP*CP*G)-3'): “The structure of a B-DNA decamer with a central T-a step: C- G-a-T-T-a-a-T-C-G”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.25). MolNFT v1 #3825 on GenesisL1: 3D…

PDB: 1D49
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*AP*TP*TP*AP*AP*TP*CP*G)-3')
Ligands: MG
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

MG · Magnesium ion · metal · 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	59	0.25	0.72	15	MG

Interfaces

1 interface between chains.

A–B · 466 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Compared structures

1D49 · The structure of a B-DNA decamer with a central T-a step: C-G-a-T-T-a-a-T-C-G · 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 1D49 · PDBe 1D49

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