1C0Q

COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID

• PDB DOI: https://doi.org/10.2210/pdb1C0Q/pdb

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


• Deposited: 1999-07-20 Released: 1999-07-30 
• Deposition Author(s): Loll, P.J., Kaplan, J., Selinsky, B., Axelsen, P.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.119 
• R-Value Observed: 0.119 

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.14 kDa 
• Atom Count: 269 
• 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
LAC	H [auth B]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N
CL	E [auth A], 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: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.119 
• R-Value Observed: 0.119 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.4	α = 90
b = 28.4	β = 90
c = 65.73	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-30 
Deposition Author(s): Loll, P.J., Kaplan, J., Selinsky, B., Axelsen, P.H.

Revision History  

• Version 1.0: 1999-07-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  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 1.5: 2013-03-27
  Changes: Structure summary
• Version 1.6: 2013-04-10
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Polymer sequence, Refinement description, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary