Research workbench
2.4 ångström crystal structure of the asymmetric platinum complex {PT(AMMINE)(CYCLOHEXYLAMINE)}2+ bound to a dodecamer DNA duplex
Analyse 2.4 ångström crystal structure of the asymmetric platinum complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LU5
- 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
- LPT
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3' | dna | 12 | — | — |
| B, D | 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- LPT · Cis-(ammine)(cyclohexylamine)platinum(ii) complex · ligand · 2 copies · chains A, B, C, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.32 | 0.72 | 11 | LPT |
| 2 | 66 | 0.25 | 0.72 | 11 | LPT |
Interfaces
3 interfaces between chains.
- A–B · 563 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–D · 563 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–C · 113 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 1LU5 · 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex… · 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 1LU5 · PDBe 1LU5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.