MolNFT v1 · #169458 · DNA

Crystal structure of human telomeric DNA G-quadruplex in complex with a novel PLATINUM(II) complex.

6XCL · DNA (5'- D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*…: “Crystal structure of human telomeric DNA G-quadruplex in complex with a novel PLATINUM(II) complex.”. X-ray diffraction, 2 ligands (V4A, K), 1 pocket (best druggability…

PDB: 6XCL
Type: DNA
Length: 44 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)- 3')
Ligands: V4A, K
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'- D(APGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPG)- 3')	dna	22	—	—

Ligands and binding sites

V4A · Platinum(II) bis[3-(pyridin-2-yl)-[1,2,4]triazolo[4,3-a]pyridine] · ligand · 3 copies · chains A, B
K · Potassium ion · metal · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	809	0.78	0.82	36	V4A

Interfaces

1 interface between chains.

A–B · 492 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Compared structures

6XCL · Crystal Structure of human telomeric DNA G-quadruplex in complex with a novel… · 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 6XCL · PDBe 6XCL

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