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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of a hydrated gramicidin S urea complex

(1978) Nature 275: 206-207

Macromolecule Content

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URE Query on URE Download:Ideal Coordinates CCD File SDF format, chain B [auth D] MOL2 format, chain B [auth D] mmCIF format, chain B [auth D]	B [auth D]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPN Query on DPN	A [auth D]	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		--
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		Interactions Focus chain A [auth D] Interactions & Density Focus chain A [auth D]

Experimental Data & Validation

Experimental Data

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

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.