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- PDB-1ao2: cobalt(III)-deglycopepleomycin determined by NMR studies -

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Basic information

Entry
Database: PDB / ID: 1ao2
Titlecobalt(III)-deglycopepleomycin determined by NMR studies
Components
  • (0) x AGLYCON OF PEPLOMYCIN
  • (1) x COBALT (III) ION
  • (2) x HYDROGEN PEROXIDE
KeywordsINHIBITOR / anticancer drugs / deglycosylated pepleomycin / peplomycin / bleomycin / DNA / two-dimensional NMR / solution structures
Function / homologyCOBALT (III) ION / HYDROGEN PEROXIDE / AGLYCON OF PEPLOMYCIN
Function and homology information
MethodSOLUTION NMR
AuthorsCaceres-Cortes, J. / Sugiyama, H. / Ikudome, K. / Saito, I. / Wang, A.H.-J.
CitationJournal: Eur.J.Biochem. / Year: 1997
Title: Structures of cobalt(III)-pepleomycin and cobalt(III)-deglycopepleomycin (green forms) determined by NMR studies.
Authors: Caceres-Cortes, J. / Sugiyama, H. / Ikudome, K. / Saito, I. / Wang, A.H.
History
DepositionJul 16, 1997Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1993
Polymers00
Non-polymers1,1993
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1minimal energy
RepresentativeModel #1minimized average

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Components

#1: Chemical ChemComp-PMY / AGLYCON OF PEPLOMYCIN / AGLYCON OF (S)-N1-[3-[(1-PHENYLETHYL)AMINO]-PROPYL]BLEOMYCINAMIDE


Mass: 1106.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H67N17O10S2
#2: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
Details: a derivative of bleomycin from Streptomyces verticillus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
131DQF-COSY
NMR detailsText: method used to determine the structure : NOE-RMD

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Sample preparation

DetailsContents: 50mM sodium phosphate, 0.15 M NaCl / Solvent system: H2O
Sample conditionspH: 6.4 / Pressure: 1 atm / Temperature: 275 K

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NMR measurement

NMR spectrometerType: Varian VXR 500 / Manufacturer: Varian / Model: VXR 500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1A.T.Brungerrefinement
SPEDREFrefinement
RefinementSoftware ordinal: 1
Details: Refinement details can be found in the JRNL citation
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: minimal energy / Conformers calculated total number: 1 / Conformers submitted total number: 1

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