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- PDB-1dsr: Peptide antibiotic, NMR, 6 structures -

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Basic information

Entry
Database: PDB / ID: 1dsr
TitlePeptide antibiotic, NMR, 6 structures
ComponentsRAMOPLANIN A2
KeywordsANTIBIOTIC / RAMOPLANIN / INHIBITOR / GLYCOLIPODESPSIPEPTIDE
Function / homologyRAMOPLANIN A2 / (2Z,4E)-7-methylocta-2,4-dienoic acid / :
Function and homology information
Biological speciesACTINOPLANES SP. (bacteria)
MethodSOLUTION NMR
AuthorsKurz, M. / Guba, W.
CitationJournal: Biochemistry / Year: 1996
Title: 3D Structure of Ramoplanin: A Potent Inhibitor of Bacterial Cell Wall Synthesis.
Authors: Kurz, M. / Guba, W.
History
DepositionJul 5, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAMOPLANIN A2
A: (2Z,4E)-7-methylocta-2,4-dienoic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6083
Polymers2,1121
Non-polymers4972
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 450ENERGY MINIMIZED SNAPSHOT EVERY 75 PS
Representative

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Components

#1: Protein/peptide RAMOPLANIN A2 / A-166686 / MDL 62 / 198)


Type: Lipoglycopeptide / Class: Antibiotic / Mass: 2111.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: RAMOPLANIN A2 IS A CYCLIC HEPTADECAMER LIPOGLYCODEPSIPEPTIDE. THE SCAFFOLD IS A HEPTA CYCLIC PEPTIDE GLYCOSYLATED BY ONE DISACCHARIDE AND A FATTY ACID AT THE N-TERM.
Source: (natural) ACTINOPLANES SP. (bacteria) / Strain: ATCC 33076 / References: NOR: NOR00844, RAMOPLANIN A2
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Lipoglycopeptide / Class: Antibiotic / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RAMOPLANIN A2 IS A CYCLIC HEPTADECAMER LIPOGLYCODEPSIPEPTIDE. THE SCAFFOLD IS A HEPTA CYCLIC PEPTIDE GLYCOSYLATED BY ONE DISACCHARIDE AND A FATTY ACID AT THE N-TERM.
References: RAMOPLANIN A2
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-FA7 / (2Z,4E)-7-methylocta-2,4-dienoic acid


Type: Lipoglycopeptide / Class: Antibiotic / Mass: 154.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14O2
Details: RAMOPLANIN A2 IS A CYCLIC HEPTADECAMER LIPOGLYCODEPSIPEPTIDE. THE SCAFFOLD IS A HEPTA CYCLIC PEPTIDE GLYCOSYLATED BY ONE DISACCHARIDE AND A FATTY ACID AT THE N-TERM.
References: RAMOPLANIN A2
Compound detailsRAMOPLANIN IS A CYCLIC LIPOGLYCOPEPTIDE. HERE, RAMOPLANIN IS REPRESENTED BY GROUPING TOGETHER THE ...RAMOPLANIN IS A CYCLIC LIPOGLYCOPEPTIDE. HERE, RAMOPLANIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) A FATTY ACID (FA7) AND TWO LIGANDS (HET) MAN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

Sample conditionspH: 4.6 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz

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Processing

NMR ensembleConformer selection criteria: ENERGY MINIMIZED SNAPSHOT EVERY 75 PS
Conformers calculated total number: 450 / Conformers submitted total number: 6

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