Download MendeleyThe crystal structure of a hydrated gramicidin S urea complex
Dodson, E.J.(1978) Nature 275: 206-207
8RC7
The structure of membrane-active antibiotic cyclodecapeptide gramicidin S in complex with urea
- PDB DOI: https://doi.org/10.2210/pdb8RC7/pdb
- Classification: ANTIBIOTIC
- Organism(s): Brevibacillus brevis
- Mutation(s): No
- Deposited: 2023-12-06 Released: 2024-03-06
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.132
- R-Value Work: 0.140
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Gramicidin S | A [auth D] | 10 | Brevibacillus brevis | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| URE Query on URE | B [auth D] | UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ORN Query on ORN | A [auth D] | L-PEPTIDE LINKING | C5 H12 N2 O2 |  | ALA |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000219 Query on PRD_000219 | A [auth D] | GRAMICIDIN S | Cyclic peptide / Antibiotic |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.132
- R-Value Work: 0.140
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 25.8 | α = 90 |
| b = 25.8 | β = 90 |
| c = 21.49 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-03-06 Deposition Author(s): Dodson, E.J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-03-06
Type: Initial release
