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X-ray structure of the a-decamer gcgtatacgc with a single 2'-O-butyl thymine in place of T6, sr-form

Analyse X-ray structure of the a-decamer gcgtatacgc with a single 2'-O-butyl thymine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WV6
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*(2BT)P*AP*CP*GP*C)-3'
Ligands: SR
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GPCPGPTPAP(2BT)PAPCPGPC)-3'	dna	10	—	—

Ligands and binding sites

SR · Strontium ion · metal · 5 copies · chains B, 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	102	0.31	0.72	13	SR

Interfaces

1 interface between chains.

A–B · 479 Å² buried · 49 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1WV6 · X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of… · 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 1WV6 · PDBe 1WV6

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