MolNFT v1 · #28292 · DNA

Crystal structure of the a-DNA GCGTATCGC with a 2'-O- propargyl thymidine (T)

1Y9S · 5'-D(*GP*CP*GP*TP*AP*(2GT)P*AP*CP*GP*C)-3'): “Crystal structure of the a-DNA GCGTAT*CGC with a 2'-O- propargyl thymidine (T*)”. X-ray diffraction, 1 pocket (best druggability 0.28). MolNFT v1 #28292 on GenesisL1: 3D structure…

PDB: 1Y9S
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*(2GT)P*AP*CP*GP*C)-3')
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GPCPGPTPAP(2GT)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	88	0.28	0.72	13	empty

Interfaces

1 interface between chains.

A–B · 486 Å² buried · 34 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1Y9S · Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*) · 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 1Y9S · PDBe 1Y9S

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