MolNFT v1 · #148323 · DNA
The cytotoxic [PT(H2BAPBPY)] platinum complex interacting with the cgtacg hexamer
6F3C · DNA (5'-D(*GP*TP*AP*CP*G)-3'): “The cytotoxic [PT(H2BAPBPY)] platinum complex interacting with the cgtacg hexamer”. X-ray diffraction, 2 ligands (PT9, MG). MolNFT v1 #148323 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6F3C
- Type
- DNA
- Length
- 22 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*TP*AP*CP*G)-3')
- Ligands
- PT9, MG
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA (5'-D(*GP*TP*AP*CP*G)-3') | dna | 6 | — | — |
| C, A | DNA (5'-D(*GP*TP*AP*CP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- PT9 · [Pt(H2bapbpy)] platinum · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–A · 186 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- B–C · 185 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- D–C · 185 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–D · 175 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- D–A · 170 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 6F3C · The cytotoxic [Pt(H2bapbpy)] platinum complex interacting with the CGTACG hexamer · the same entry in another collection · chain B against B, 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 6F3C · PDBe 6F3C
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