1SHO

CRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Observed: 0.105 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of Vancomycin.

Schafer, M.Schneider, T.R.Sheldrick, G.M.

(1996) Structure 4: 1509

  • DOI: 10.1016/s0969-2126(96)00156-6
  • Primary Citation of Related Structures:  
    1SHO

  • PubMed Abstract: 
  • Vancomycin and other related glycopeptide antibiotics are clinically very important because they often represent the last line of defence against bacteria that have developed resistance to antibiotics. Vancomycin is believed to act by binding nascent cell wall mucopeptides terminating in the sequence D-Ala-D-Ala, weakening the resulting cell wall ...

    Vancomycin and other related glycopeptide antibiotics are clinically very important because they often represent the last line of defence against bacteria that have developed resistance to antibiotics. Vancomycin is believed to act by binding nascent cell wall mucopeptides terminating in the sequence D-Ala-D-Ala, weakening the resulting cell wall. Extensive NMR and other studies have shown that the formation of asymmetric antibiotic dimers is important in peptide binding. Despite intensive efforts the crystal structure of vancomycin has been extremely difficult to obtain, partly because high-resolution data were unavailable, and partly because the structure was too large to be solved by conventional "direct methods'.


    Organizational Affiliation

    Institut für Anorganische Chemie, Universität Göttingen, Germany.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VANCOMYCINA, B7Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
vancosamine-(1-2)-beta-D-glucopyranoseC, D2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14263HU
GlyCosmos:  G14263HU
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B], G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMY
Query on OMY
A, BL-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
A, BVancomycinGlycopeptide /  Antibiotic Ligand Interaction
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
C, DVancomycinGlycopeptide /  Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Observed: 0.105 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.48α = 90
b = 28.48β = 90
c = 65.83γ = 90
Software Package:
Software NamePurpose
SHELX-96model building
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELX-96phasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1997-07-23 
  • Released Date: 1997-12-24 
  • Deposition Author(s): Sheldrick, G.M.

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-24
    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: Atomic model, Data collection, Derived calculations, Other, Polymer sequence, Structure summary