MolNFT v1 · #27838 · protein + DNA
Echinomycin (CGTACG)2 complex
1XVR · 5'-D(*CP*GP*TP*AP*CP*G)-3': “Echinomycin (CGTACG)2 complex”. X-ray diffraction, 2 ligands (QUI, MG). MolNFT v1 #27838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XVR
- Type
- protein + DNA
- Length
- 28 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*TP*AP*CP*G)-3'; Echinomycin
- Ligands
- QUI, MG
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-D(*CP*GP*TP*AP*CP*G)-3' | dna | 6 | — | — |
| D, E | Echinomycin | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- QUI · 2-carboxyquinoxaline · ligand · 4 copies · chains A, C, D, E
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–C · 278 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- C–E · 196 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–E · 187 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–D · 186 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 184 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified, 4 covalent, 4 d-amino (covalent ligand, D-amino acid, methylation, nonstandard).
Compared structures
- 1XVR · echinomycin (CGTACG)2 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 1XVR · PDBe 1XVR
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