MolNFT v1 · #21251 · DNA

Crystal structure analysis of the DNA quadruplex D(TGGGGT)S2

1S47 · 5'-D(*TP*GP*GP*GP*GP*T)-3': “Crystal structure analysis of the DNA quadruplex D(TGGGGT)S2”. X-ray diffraction, 2 ligands (NA, TL). MolNFT v1 #21251 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1S47
Type: DNA
Length: 68 nucleotides
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*GP*GP*GP*GP*T)-3'
Ligands: NA, TL

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J, L	5'-D(TPGPGPGPGPT)-3'	dna	5	—	—
B, C, D, E, F, H, I, K	5'-D(TPGPGPGPGPT)-3'	dna	6	—	—

Ligands and binding sites

NA · Sodium ion · metal · 7 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
TL · Thallium (I) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

31 interfaces between chains.

J–K · 292 Å² buried · 15 hydrogen bonds · nucleic-nucleic
F–L · 292 Å² buried · 8 hydrogen bonds · nucleic-nucleic
B–C · 291 Å² buried · 21 hydrogen bonds · nucleic-nucleic
G–K · 289 Å² buried · 11 hydrogen bonds · nucleic-nucleic
I–L · 283 Å² buried · 13 hydrogen bonds · nucleic-nucleic

Compared structures

1S47 · Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2 · 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 1S47 · PDBe 1S47

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