Research workbench
Intercalation of an 9ACRIDINE-peptide drug in a DNA dodecamer
Analyse Intercalation of an 9ACRIDINE-peptide drug in a DNA dodecamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G3X
- Type
- protein + DNA
- Length
- 147 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'; N(ALPHA)-(9-acridinoyl)-tetraarginine-amide
- Ligands
- 9AC, MG
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, K, L | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | dna | 12 | — | — |
| G | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | dna | 11 | — | — |
| M | N(ALPHA)-(9-acridinoyl)-tetraarginine-amide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 9AC · 9-acridinecarbonyl · ligand · chains K, L, M
- MG · Magnesium ion · metal · 7 copies · chains A, B, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.53 | 0.73 | 35 | empty |
| 2 | 112 | 0.34 | 0.73 | 9 | empty |
| 3 | 64 | 0.28 | 0.74 | 12 | empty |
| 4 | 63 | 0.26 | 0.72 | 6 | empty |
| 5 | 52 | 0.23 | 0.72 | 13 | empty |
Interfaces
15 interfaces between chains.
- E–F · 583 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- C–D · 581 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- I–J · 576 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–B · 569 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- G–H · 551 Ų buried · 63 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1G3X · Intercalation of an 9ACRIDINE-peptide drug in a DNA dodecamer · 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 1G3X · PDBe 1G3X
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