MolNFT v1 · #14894 · protein + DNA
Actinomycin D binding to atgctgcat
1MNV · 5'-D(*AP*TP*GP*CP*TP*GP*CP*AP*T)-3': “Actinomycin D binding to atgctgcat”. X-ray diffraction, 1 ligand (PXZ). MolNFT v1 #14894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1MNV
- Type
- protein + DNA
- Length
- 38 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*GP*CP*TP*GP*CP*AP*T)-3'; Actinomycin D
- Ligands
- PXZ
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*AP*TP*GP*CP*TP*GP*CP*AP*T)-3' | dna | 9 | — | — |
| C, D | 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 · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- A–B · 436 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–D · 266 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 262 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–D · 254 Ų buried · 1 hydrogen bond · protein-nucleic
- A–C · 213 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified, 4 covalent, 4 d-amino (methylation, covalent ligand, D-amino acid).
Compared structures
- 1MNV · Actinomycin D binding to ATGCTGCAT · 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 1MNV · PDBe 1MNV
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