Download MendeleyCrystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex
Lee, Y.Y., Hou, M.H.To be published.
8YS7 | pdb_00008ys7
Crystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex
- PDB DOI: https://doi.org/10.2210/pdb8YS7/pdb
- NAKB: 8YS7
- Classification: DNA/ANTIBIOTIC
- Organism(s): synthetic construct, Streptomyces
- Mutation(s): No
- Deposited: 2024-03-22 Released: 2025-04-09
- Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.24 Å
- R-Value Free: 0.292 (Depositor), 0.292 (DCC)
- R-Value Work: 0.277 (Depositor), 0.278 (DCC)
- R-Value Observed: 0.279 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Echinomycin | E, H [auth A] | 8 | Streptomyces | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| actinomycin D | F [auth I], G [auth D] | 11 | Streptomyces | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*GP*CP*CP*CP*CP*GP*T)-3') | A [auth B], C [auth K] | 8 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3') | B [auth C], D [auth L] | 7 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| QUI (Subject of Investigation/LOI) Query on QUI | I [auth E], J [auth E], K [auth A], L [auth A] | 2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MVA Query on MVA | E, H [auth A] | L-PEPTIDE LINKING | C6 H13 N O2 |  | VAL |
| SAR Query on SAR | F [auth I], G [auth D] | PEPTIDE LINKING | C3 H7 N O2 |  | GLY |
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000491 Query on PRD_000491 | E [auth A], H [auth E] | Echinomycin | Cyclic depsipeptide / Antibiotic |  | |
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000001 Query on PRD_000001 | F [auth D], G [auth I] | Actinomycin D | Polypeptide / Antibiotic |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.24 Å
- R-Value Free: 0.292 (Depositor), 0.292 (DCC)
- R-Value Work: 0.277 (Depositor), 0.278 (DCC)
- R-Value Observed: 0.279 (Depositor)
Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 132.661 | α = 90 |
| b = 132.661 | β = 90 |
| c = 50.052 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Science and Technology (MoST, Taiwan) | Taiwan | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-04-09
Type: Initial release
