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Crystal structure of a-DNA decamer GCGTA(3ME)ACGC, with a modified 5- methyluridine

Analyse Crystal structure of a-DNA decamer GCGTA(3ME)ACGC, with a modified 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NZG
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*(3ME)P*AP*CP*GP*C)-3'
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(3ME)PAPCPGPC)-3'	dna	10	—	—

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	101	0.30	0.72	14	empty

Interfaces

1 interface between chains.

A–B · 486 Å² buried · 42 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1NZG · Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1NZG · PDBe 1NZG

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