Research workbench
Crystal structure of echinomycin-D(ACGTCGT)2 complex
Analyse Crystal structure of echinomycin-D(ACGTCGT)2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YTZ
- Type
- protein + DNA
- Length
- 30 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3'); Echinomycin
- Ligands
- QUI, MN, K
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3') | dna | 7 | — | — |
| D, F | Echinomycin | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- QUI · 2-carboxyquinoxaline · ligand · 4 copies · chains A, B, D, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- A–B · 338 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- A–F · 245 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 231 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–F · 228 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 221 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified, 4 covalent, 4 d-amino (covalent ligand, D-amino acid, methylation, nonstandard, nucleotide modification).
Compared structures
- 5YTZ · Crystal structure of echinomycin-d(ACGTCGT)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 5YTZ · PDBe 5YTZ
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