+Open data
-Basic information
Entry | Database: PDB / ID: 6v1j | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of KPC-2 bound to QPX7728 at 1.30 A | ||||||
Components | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Pemberton, O.A. / Chen, Y. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases. Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6v1j.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v1j.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 6v1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v1j_validation.pdf.gz | 413.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6v1j_full_validation.pdf.gz | 415.4 KB | Display | |
Data in XML | 6v1j_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6v1j_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/6v1j ftp://data.pdbj.org/pub/pdb/validation_reports/v1/6v1j | HTTPS FTP |
-Related structure data
Related structure data | 6v1mC 6v1oC 6v1pC 5ul8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30806.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F663, beta-lactamase |
---|
-Non-polymers , 5 types, 328 molecules
#2: Chemical | ChemComp-RM9 / ( | ||
---|---|---|---|
#3: Chemical | ChemComp-QNA / ( | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45.34 Å / Num. obs: 65033 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.99 / Num. measured all: 21968 / Num. unique obs: 3161 / CC1/2: 0.638 / Net I/σ(I) obs: 1.8 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | ||||||
---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UL8 Resolution: 1.3→40.8 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.75
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.92 Å2 / Biso mean: 16.4974 Å2 / Biso min: 6.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→40.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
|