Download MendeleyCrystal structures and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family
Heck, T., Merz, T., Geueke, B., Gruetter, M.G., Kohler, H.-P.E.To be published.
3NDV
Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin
- PDB DOI: https://doi.org/10.2210/pdb3NDV/pdb
- Classification: HYDROLASE/ANTIBIOTIC
- Organism(s): Sphingosinicella xenopeptidilytica
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-06-08 Released: 2011-09-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.192
- R-Value Work: 0.167
- R-Value Observed: 0.168
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-peptidyl aminopeptidase | 373 | Sphingosinicella xenopeptidilytica | Mutation(s): 0 Gene Names: bapA EC: 3.4.11.25 |  | |
UniProt | |||||
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica) Explore Q52VH2 Go to UniProtKB: Q52VH2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q52VH2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NDV Query on NDV | G [auth A], N [auth D] | (2S,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C16 H21 N3 O4 S WHAIWIUXAXKSOT-NMKXLXIOSA-N |  | ||
| AIC Query on AIC | F [auth A], J [auth B], L [auth C], M [auth D] | (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC
ACID C16 H19 N3 O4 S AVKUERGKIZMTKX-NJBDSQKTSA-N |  | ||
| GOL Query on GOL | E [auth A], H [auth B], I [auth B], K [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.192
- R-Value Work: 0.167
- R-Value Observed: 0.168
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.9 | α = 90 |
| b = 96.4 | β = 108.4 |
| c = 101.5 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2011-09-28 Deposition Author(s): Merz, T., Heck, T., Geueke, B., Kohler, H.-P.E., Gruetter, M.G.
Revision History (Full details and data files)
- Version 1.0: 2011-09-28
Type: Initial release - Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
