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The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-a-a-T-T-C-G-C-G

Analyse The primary mode of binding of cisplatin to a B-DNA dodecamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BNA
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)- 3')
Ligands: PTN
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)- 3')	dna	12	—	—

Ligands and binding sites

PTN · Platinum triamine ion · ligand · 3 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.28	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 571 Å² buried · 61 hydrogen bonds · nucleic-nucleic

Compared structures

5BNA · The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-a-a-T-T-C-G-C-G · 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 5BNA · PDBe 5BNA

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