1GAC

NMR structure of asymmetric homodimer of a82846b, a glycopeptide antibiotic, complexed with its cell wall pentapeptide fragment


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 80 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Conformation of A82846B, a Glycopeptide Antibiotic, Complexed with its Cell Wall Fragment: An Asymmetric Homodimer Determined Using NMR Spectroscopy.

Prowse, W.G.Kline, A.D.Skelton, M.A.Loncharich, R.J.

(1995) Biochemistry 34: 9632

  • DOI: 10.1021/bi00029a041
  • Primary Citation of Related Structures:  
    1GAC

  • PubMed Abstract: 
  • Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols ...

    Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols. These structures were subsequently refined using the full CHARMm potential and the addition of water molecules in the calculation. The CHARMm structures occupied more conformational space than did the X-PLOR structures and were utilized for the structure analysis. From the structures, a unique set of interactions for the dALA-5 carboxylate pocket was observed, having backbone amides from residues 2 and 3 hydrogen bonding one carboxylate oxygen while amide 4 and the side chain amide from Asn-3 hydrogen bond the other oxygen. Also, near the N-terminal region of the ligand, the GGLU-2's carboxylate forms a hydrogen bond with the asymmetric disaccharide dyad, which helps to define the interactions seen for this part of the ligand.


    Organizational Affiliation

    Lilly Research Laboratory, Eli Lilly and Company, Indianapolis, Indiana46285-0403, USA.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL WALL PENTAPEPTIDEA, B5Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CHLOROORIENTICIN AC, D7Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
vancosamine-(1-2)-beta-D-glucopyranoseE, F2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14263HU
GlyCosmos:  G14263HU
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RER (Subject of Investigation/LOI)
Query on RER

Download Ideal Coordinates CCD File 
G [auth C], H [auth D]vancosamine
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMY
Query on OMY
C, DL-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000203
Query on PRD_000203
C, DChloroorienticin AGlycopeptide / Antibiotic Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000203
Query on PRD_000203
E, FChloroorienticin AGlycopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 80 
  • OLDERADO: 1GAC Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Polymer sequence, Structure summary