Research workbench
Crystal structure of a 7-aminoactinomycin D complex with non- complementary DNA
Analyse Crystal structure of a 7-aminoactinomycin D complex with non- complementary DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UNJ
- Type
- protein + DNA
- Length
- 153 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*AP*GP*BRU*TP)-3'; 7-amino-actinomycin D
- Ligands
- PX1
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 5 | — | — |
| B, H, N, T | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 4 | — | — |
| C, I, O, U | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 4 | — | — |
| E, F, K, L, Q, R, W, X | 7-amino-actinomycin D | protein | 10 | 0% helix, 20% strand | — |
| V | 5'-D(*TP*TP*AP*GP*BRU*TP)-3' | dna | 6 | — | — |
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 · 8 copies · chains A, C, E, B, D, F, G, I, K, H, J, L, M, O, Q, N, P, R, S, U, W, T, V, X
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 | 54 | 0.36 | 0.80 | 10 | PX1 |
Interfaces
64 interfaces between chains.
- M–Q · 263 Ų buried · 2 hydrogen bonds · protein-nucleic
- G–K · 262 Ų buried · 2 hydrogen bonds · protein-nucleic
- S–W · 259 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–E · 258 Ų buried · 2 hydrogen bonds · protein-nucleic
- T–V · 256 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 48 modified, 16 covalent, 16 d-amino (methylation, covalent ligand, D-amino acid, nucleotide modification).
Compared structures
- 1UNJ · Crystal structure of a 7-Aminoactinomycin D complex 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 1UNJ · PDBe 1UNJ
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