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Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster (T5A mutant)

Analyse Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster (T5A mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BSE
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')
Ligands: AG, CA
Pockets: 1 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(CPAPCPCPAPAPGPCPGPA)-3')	dna	10	—	—

Ligands and binding sites

AG · Silver ion · metal · 36 copies · chains A, B, C, D
CA · Calcium ion · metal · 8 copies · chains B, C

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	305	0.68	0.84	17	CA

Interfaces

3 interfaces between chains.

A–B · 362 Å² buried · 21 hydrogen bonds · nucleic-nucleic
C–D · 361 Å² buried · 20 hydrogen bonds · nucleic-nucleic
B–C · 144 Å² buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

7BSE · Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5A mutant) · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7BSE · PDBe 7BSE

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