1AA5

VANCOMYCIN

• PDB DOI: https://doi.org/10.2210/pdb1AA5/pdb

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


• Deposited: 1997-01-23 Released: 1997-08-20 
• Deposition Author(s): Loll, P.J., Bevivino, A.E., Korty, B.D., Axelsen, P.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.89 Å
• R-Value Observed: 0.124 

Literature

Simultaneous Recognition of a Carboxylate-Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer.

Loll, P.J., Bevivino, A.E., Korty, B.D., Axelsen, P.H.

(1997) J Am Chem Soc 119: 1516

• DOI: https://doi.org/10.1021/JA963566P

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.15 kDa 
• Atom Count: 284 
• 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
Glycosylation
Glycosylation Sites: 1

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
ACY	E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth B], I [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: 0.89 Å
• R-Value Observed: 0.124 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.45	α = 90
b = 28.45	β = 90
c = 65.84	γ = 90

Software Package:

Software Name	Purpose
SHELXL-93	model building
SHELXL-93	refinement
MADNES	data reduction
PROCOR	data reduction
XSCALE	data scaling
SHELXL-93	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-08-20 
Deposition Author(s): Loll, P.J., Bevivino, A.E., Korty, B.D., Axelsen, P.H.

Revision History  

• Version 1.0: 1997-08-20
  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 1.5: 2016-10-19
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Polymer sequence, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary