1GO6

Balhimycin in complex with Lys-D-ala-D-ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Structures of Glycopeptide Antibiotics with Peptides that Model Bacterial Cell-Wall Precursors

Lehmann, C.Bunkoczi, G.Vertesy, L.Sheldrick, G.M.

(2002) J.Mol.Biol. 318: 723

  • DOI: 10.1016/S0022-2836(02)00146-8
  • Primary Citation of Related Structures:  1HHU, 1HHY, 1HHZ

  • PubMed Abstract: 
  • The vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (<1 A). In addi ...

    The vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (<1 A). In addition to the features expected from previous structural and spectroscopic studies, two new motifs were observed that may prove important in the design of antibiotics modified to overcome bacterial resistance. A changed binding mode was found in two dipeptide complexes, and a new type of face-to-face oligomerization (in addition to the well-established back-to-back dimerization) was seen when the model peptide reaches a critical fraction of the size of the cell-wall precursor pentapeptide. The extensive interactions involving both antibiotic and peptide molecules in this interface should appreciably enhance the kinetic and thermodynamic stability of the complexes. In the pentapeptide complex, the relative positions of the peptides are close to those required for d-Ala elimination, so this structure may provide a realistic model for the prevention of the enzyme-catalyzed cell-wall crosslinking by antibiotic binding.


    Organizational Affiliation

    Lehrstuhl für Strukturchemie, Institute für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BALHIMYCIN
A, C, E, G, I, K, M, O
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE LYS-DAL-DAL
B, D, F, H
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
E, I, K, M, O
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A, C, E, G, I, K, M, O
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
I
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
DVC
Query on DVC

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
(2R,4S,6S)-4-azanyl-4,6-dimethyl-oxane-2,5,5-triol
C7 H15 N O4
ATGUYZRYRGIDLC-JKUQZMGJSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
K
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000484
Query on PRD_000484
A,C,E,G,I,K,M,OBalhimycinGlycopeptide / Antibiotic, Antimicrobial

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DAL
Query on DAL
B, D, F, H
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.927α = 90.00
b = 28.025β = 90.00
c = 50.707γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SHELXDphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-07-25
    Type: Atomic model, Non-polymer description, Other
  • Version 1.3: 2012-11-30
    Type: Other
  • Version 1.4: 2013-02-27
    Type: Derived calculations
  • Version 1.5: 2013-03-20
    Type: Derived calculations
  • Version 1.6: 2017-02-08
    Type: Source and taxonomy