8RC7 | pdb_00008rc7

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 
• Deposition Author(s): Dodson, E.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.132 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.150 (DCC) 

Literature

The crystal structure of a hydrated gramicidin S urea complex

Dodson, E.J.

(1978) Nature 275: 206-207

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1.22 kDa 
• Atom Count: 102 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gramicidin S	A [auth D]	10	Brevibacillus brevis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URE	B [auth D]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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	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 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.150 (DCC) 

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 Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Dodson, E.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release