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X-ray crystal structure of duplex DNA containing a cisplatin 1,2- D(GPG) intrastrand cross-link

Analyse X-ray crystal structure of duplex DNA containing a cisplatin 1,2- D(GPG)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3LPV
Type
DNA
Length
48 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'; 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'
Ligands
CPT, MG
Pockets
2 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, C5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'dna12——
B, D5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'dna12——

Ligands and binding sites

  • CPT · Cisplatin · ligand · 2 copies · chains A, C
  • MG · Magnesium ion · metal · 4 copies · chains B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11000.320.739CPT
21010.300.7110CPT

Interfaces

3 interfaces between chains.

  • A–B · 570 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • C–D · 568 Ų buried · 54 hydrogen bonds · nucleic-nucleic
  • A–C · 116 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 3LPV · X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand… · the same entry in another collection · chain A against A, TM-score 1.00

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