Research workbench
Cyclopentane peptide nucleic acid in complex with DNA
Analyse Cyclopentane peptide nucleic acid in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZL
- Type
- DNA
- Length
- 9 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3')
- Ligands
- XDJ, XDD, XDY, XDV, ZN, IOD
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3') | dna | 9 | — | — |
Ligands and binding sites
- XDJ · N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine · ligand · 3 copies · chains A
- XDD · N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine · ligand · 3 copies · chains A
- XDY · N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine · ligand · 3 copies · chains A
- XDV · 2-[2-(2-aminoethoxy)ethoxy]acetamide · ligand
- ZN · Zinc ion · metal · 6 copies · chains A
- IOD · Iodide ion · ion · chains A
- MOH · Methanol · additive · 3 copies
- EDO · 1,2-ethanediol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7KZL · Cyclopentane peptide nucleic acid in complex with DNA · 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 7KZL · PDBe 7KZL
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