MolNFT v1 · #153010 · protein + DNA
Crystal structure of actinomycin D- D(TTGGCGAA) complex
6J0H · DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3'): “Crystal structure of actinomycin D- D(TTGGCGAA) complex”. X-ray diffraction, 2 ligands (PXZ, NA). MolNFT v1 #153010 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6J0H
- Type
- protein + DNA
- Length
- 18 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3'); Actinomycin D
- Ligands
- PXZ, NA
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3') | dna | 8 | — | — |
| B | Actinomycin D | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- PXZ · 2-amino-1,9-dicarbonyl-4,6-dimethyl-10-dehydro-phenoxazin-3-one · ligand · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 236 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino (methylation, covalent ligand, D-amino acid).
Compared structures
- 6J0H · Crystal structure of Actinomycin D- d(TTGGCGAA) 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 6J0H · PDBe 6J0H
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