MolNFT v1 · #24204 · protein + DNA
Crystal structure of 7-aminoactinomycin D with non-complementary DNA
1UNM · 5'-D(*TP*TP*AP*GP*BRU*TP)-3': “Crystal structure of 7-aminoactinomycin D with non-complementary DNA”. X-ray diffraction, 1 ligand (PX1), 1 pocket (best druggability 0.29). MolNFT v1 #24204 on GenesisL1: 3D structure, binding sites…
- PDB
- 1UNM
- Type
- protein + DNA
- Length
- 39 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*AP*GP*BRU*TP)-3'; 7-aminoactinomycin D
- Ligands
- PX1
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 6 | — | — |
| B | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 4 | — | — |
| C | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 4 | — | — |
| D | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 5 | — | — |
| E, F | 7-aminoactinomycin D | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- PX1 · (1Z)-7-amino-1-(hydroxymethylene)-2-imino-4,6-dimethyl-3-oxo-2,3-dihydro-1H-phenoxazine-9-carbaldehyde · ligand · 2 copies · chains A, C, E, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.29 | 0.75 | 10 | PX1 |
Interfaces
13 interfaces between chains.
- A–E · 260 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–F · 244 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–D · 204 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- B–F · 156 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–E · 148 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified, 4 covalent, 4 d-amino (methylation, covalent ligand, D-amino acid, nucleotide modification).
Compared structures
- 1UNM · Crystal structure of 7-Aminoactinomycin D with non-complementary 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 1UNM · PDBe 1UNM
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