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- PDB-1grm: REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMB... -

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Entry
Database: PDB / ID: 1grm
TitleREFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodSOLUTION NMR
AuthorsArseniev, A.S. / Barsukov, I.L. / Lomize, A.L. / Orekhov, V.Y. / Bystrov, V.F.
Citation
Journal: Biol.Membr.(Ussr) / Year: 1992
Title: Refinement of the Spatial Structure of the Gramicidin a Ion Channel
Authors: Lomize, A.L. / Orekhov, V.I.U. / Arsen'Ev, A.S.
#1: Journal: FEBS Lett. / Year: 1985
Title: 1H-NMR Study of Gramicidin a Transmembrane Ion Channel. Head-to-Head Right-Handed, Single-Stranded Helices.
Authors: Arseniev, A.S. / Barsukov, I.L. / Bystrov, V.F. / Lomize, A.L. / Ovchinnikov, Yu.A.
#2: Journal: Biol.Membr.(Ussr) / Year: 1986
Title: Gramicidin a Transmembrane Ion-Channel. Three-Dimensional Structure Reconstruction Based on NMR Spectroscopy and Energy Refinement (Russian)
Authors: Arseniev, A.S. / Lomize, A.L. / Barsukov, I.L. / Bystrov, V.F.
#3: Journal: Biol.Membr.(Ussr) / Year: 1986
Title: Spatial Structure of Gramicidin a Transmembrane Ion Channel-NMR Analysis in Micelles (Russian)
Authors: Arseniev, A.S. / Barsukov, I.L. / Bystrov, V.F. / Ovchinnikov, Yu.A.
History
DepositionOct 18, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Dec 20, 2017Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure viewerMolecule:
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Assembly

Deposited unit
A: GRAMICIDIN A
B: GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Atom site foot note1: RESIDUES LEU 4, VAL 6, VAL 8, LEU 10, LEU 12, AND LEU 14 IN EACH CHAIN EXHIBIT THE D CONFIGURATION OF THE AMINO ACID.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / -
Representative

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Components

#1: Protein/peptide GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (gene. exp.) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

NMR ensembleConformers submitted total number: 5

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