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 1.4 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


  • 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 ...

    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  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL WALL PENTAPEPTIDE
A, B
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHLOROORIENTICIN A
C, D
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
C, D
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
RER
Query on RER

Download SDF File 
Download CCD File 
C, D
(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose
VANCOSAMINE
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000203
Query on PRD_000203
C,DChloroorienticin AGlycopeptide / Antibiotic

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FGA
Query on FGA
A, B
D-gamma-peptide, C-delta linkingC5 H9 N O4

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DAL
Query on DAL
A, B
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other