MolNFT v1 · #156686 · DNA

Crystal structure of a tetrameric DNA fold-back quadruplex

6MC4 · DNA (5'-D(*CP*GP*TP*CP*AP*GP*GP*CP*G)-3'): “Crystal structure of a tetrameric DNA fold-back quadruplex”. X-ray diffraction, 2 ligands (CA, K), 1 pocket (best druggability 0.65). MolNFT v1 #156686 on GenesisL1: 3D structure, binding…

PDB: 6MC4
Type: DNA
Length: 72 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*TP*CP*AP*GP*GP*CP*G)-3')
Ligands: CA, K
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	DNA (5'-D(CPGPTPCPAPGPGPCP*G)-3')	dna	9	—	—

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains A, C, G, D, E, B, F, H
K · Potassium ion · metal · chains 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	51	0.65	0.96	11	CA

Interfaces

14 interfaces between chains.

E–F · 406 Å² buried · 26 hydrogen bonds · nucleic-nucleic
C–D · 403 Å² buried · 28 hydrogen bonds · nucleic-nucleic
G–H · 399 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–B · 396 Å² buried · 26 hydrogen bonds · nucleic-nucleic
C–H · 296 Å² buried · 10 hydrogen bonds · nucleic-nucleic

Compared structures

6MC4 · Crystal structure of a tetrameric DNA fold-back quadruplex · 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 6MC4 · PDBe 6MC4

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