1AO4

COBALT(III)-PEPLOMYCIN COMPLEX DETERMINED BY NMR STUDIES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: minimal energy 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structures of cobalt(III)-pepleomycin and cobalt(III)-deglycopepleomycin (green forms) determined by NMR studies.

Caceres-Cortes, J.Sugiyama, H.Ikudome, K.Saito, I.Wang, A.H.

(1997) Eur J Biochem 244: 818-828

  • DOI: 10.1111/j.1432-1033.1997.00818.x
  • Primary Citation of Related Structures:  
    1AO4, 1AO2

  • PubMed Abstract: 
  • Pepleomycin (PEP) is a metalloglycopeptide that has stronger anticancer activity and less pulmonary toxicity than bleomycin (BLM). PEP, like BLM, exerts its action by binding to and degrading DNA in the presence of oxygen and certain metals. Obtaining detailed structural information of PEP and PEP-DNA complexes is crucial to understanding its anticancer activity ...

    Pepleomycin (PEP) is a metalloglycopeptide that has stronger anticancer activity and less pulmonary toxicity than bleomycin (BLM). PEP, like BLM, exerts its action by binding to and degrading DNA in the presence of oxygen and certain metals. Obtaining detailed structural information of PEP and PEP-DNA complexes is crucial to understanding its anticancer activity. The structures of two green forms of cobalt-PEP species, HO2-Co(III)-PEP (denoted CoPEP) and deglycosylated HO2-Co(III)-PEP (denoted CodPEP) have been obtained by NOE restrained refinements. Earlier studies of the related HO2-Co(III)-BLM A2 proposed that two chiral conformers (form A or B) could exist with either the beta-aminoalanine primary amine (A,NH2) or the mannose carbamoyl nitrogen (M,NH2) as the axial ligand. Analysis of our NOESY data shows convincingly that form A is the most probable conformer with the mannose carbamoyl M,NH2 and the beta-aminoalanine primary amine A,NH2 as the axial ligands in CoPEP and CodPEP, respectively. The NOE cross-peaks resulting from the interactions between the N-terminus (i.e., the metal-binding domain) and the C-terminus of CoPEP and CodPEP have similar patterns, suggesting that they both adopt compact structures with the bithiazole group folded back over the N-terminus.


    Organizational Affiliation

    Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.



Oligosaccharides

Help

Entity ID: 1
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3-O-carbamoyl-alpha-D-mannopyranose-(1-2)-alpha-L-gulopyranoseA2N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G34654XV
GlyCosmos:  G34654XV
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMY (Subject of Investigation/LOI)
Query on PMY

Download Ideal Coordinates CCD File 
B [auth A]AGLYCON OF PEPLOMYCIN
C48 H67 N17 O10 S2
RTKDONJKKYUNIT-HJVYYLMSSA-N
 Ligand Interaction
3CO
Query on 3CO

Download Ideal Coordinates CCD File 
C [auth A]COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
PEO
Query on PEO

Download Ideal Coordinates CCD File 
D [auth A]HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: minimal energy 
  • OLDERADO: 1AO4 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary