1GHG | pdb_00001ghg

CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON

• PDB DOI: https://doi.org/10.2210/pdb1GHG/pdb

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


• Deposited: 2000-12-13 Released: 2001-02-12 
• Deposition Author(s): Kaplan, J., Korty, B.D., Axelsen, P.H., Loll, P.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

The Role of Sugar Residues in Molecular Recognition by Vancomycin

Kaplan, J., Korty, B.D., Axelsen, P.H., Loll, P.J.

(2001) J Med Chem 44: 1837

• PubMed: 11356118 
• DOI: https://doi.org/10.1021/jm0005306
• Primary Citation Related Structures: 
  1GHG


• PubMed Abstract: 
  

  The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes. The crystal structure reveals that the aglycon binds acetate anions and forms back-to-back dimeric complexes in a manner similar to that of intact vancomycin. However, the four independent copies of the aglycon in each asymmetric unit of the crystal exhibit a high degree of conformational heterogeneity. These results suggest that the sugar residues, in addition to enlarging and strengthening the dimer interface, provide steric constraints that limit the vancomycin molecule to a relatively small number of productive conformations.

---

Organizational Affiliation: 
• Department of Pharmacology, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5 kDa 
• Atom Count: 411 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	H [auth C], J [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACY	E [auth A], F [auth B], G [auth C], I [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG	A, B, C, D	L-PEPTIDE LINKING	C8 H9 N O4		--
GHP	A, B, C, D	D-PEPTIDE LINKING	C8 H9 N O3		--
MLU	A, B, C, D	D-PEPTIDE LINKING	C7 H15 N O2		--
OMY	A, B, C, D	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR
OMZ	A, B, C, D	D-PEPTIDE LINKING	C9 H10 Cl N O4		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000206	A, B, C, D	VANCOMYCIN AGLYCON	Oligopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.150 (Depositor) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.48	α = 90
b = 29.48	β = 90
c = 74.27	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
SHELXL	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-12 
Deposition Author(s): Kaplan, J., Korty, B.D., Axelsen, P.H., Loll, P.J.

Revision History  

• Version 1.0: 2001-02-12
  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: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Polymer sequence