Download MendeleyBoric acid and acetate anion binding to subclass B3 metallo-Beta-lactamase BJP-1 provides clues for mechanism of action and inhibitor design
Di Pisa, F., Pozzi, C., Benvenuti, M., Docquier, J.-D., De Luca, F., Mangani, S.(2017) Inorganica Chim Acta
5NGG
Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion
- PDB DOI: https://doi.org/10.2210/pdb5NGG/pdb
- Classification: HYDROLASE
- Organism(s): Bradyrhizobium diazoefficiens USDA 110
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-03-17 Released: 2017-09-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.18 Å
- R-Value Free: 0.146
- R-Value Work: 0.121
- R-Value Observed: 0.122
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Blr6230 protein | 294 | Bradyrhizobium diazoefficiens USDA 110 | Mutation(s): 0 Gene Names: blr6230 |  | |
UniProt | |||||
Find proteins for Q89GW5 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89GW5 Go to UniProtKB: Q89GW5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q89GW5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A], J [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.18 Å
- R-Value Free: 0.146
- R-Value Work: 0.121
- R-Value Observed: 0.122
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 42.31 | α = 78.88 |
| b = 44.64 | β = 89.41 |
| c = 75.91 | γ = 61.99 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| iMOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2017-09-27 Deposition Author(s): Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S.
Revision History (Full details and data files)
- Version 1.0: 2017-09-27
Type: Initial release - Version 1.1: 2018-01-31
Changes: Database references, Structure summary - Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
