1SHO

CRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1SHO/pdb

• Classification: ANTIBIOTIC
• Organism(s): Amycolatopsis orientalis
• Mutation(s): No 


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

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Experimental Data Snapshot

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

Literature

Crystal Structure of Vancomycin.

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

(1996) Structure 4: 1509

• PubMed: 8994975 
• DOI: https://doi.org/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. 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'.

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Organizational Affiliation: 

Institut für Anorganische Chemie, Universität Göttingen, Germany.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.08 kDa 
• Atom Count: 318 
• Modelled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VANCOMYCIN	A, B	7	Amycolatopsis orientalis	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
vancosamine-(1-2)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G14263HU GlyCosmos:  G14263HU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMY	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204	A, B	Vancomycin	Glycopeptide / Antibiotic

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204	C, D	Vancomycin	Glycopeptide / Antibiotic

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 = 28.48	α = 90
b = 28.48	β = 90
c = 65.83	γ = 90

Software Package:

Software Name	Purpose
SHELX-96	model building
SHELXL-96	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX-96	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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