Download MendeleySimultaneous 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
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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 0.89 Å
- R-Value Observed: 0.124
wwPDB Validation 3D Report Full Report
This is version 3.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VANCOMYCIN | 7 | Amycolatopsis orientalis | Mutation(s): 0 |  | |
Glycosylation | |||||
| Glycosylation Sites: 1 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACY Query on ACY | E [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| CL Query on 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 Query on 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 Query on PRD_000204 | A, B | Vancomycin | Glycopeptide / Antibiotic |  | |
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000204 Query on 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 Name | Purpose |
|---|---|
| SHELXL-93 | model building |
| SHELXL-93 | refinement |
| MADNES | data reduction |
| PROCOR | data reduction |
| XSCALE | data scaling |
| SHELXL-93 | phasing |
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 (Full details and data files)
- 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
