[English] 日本語
![](img/lk-miru.gif)
- PDB-2y2q: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL B... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y2q | ||||||
---|---|---|---|---|---|---|---|
Title | PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z06) | ||||||
![]() | PENICILLIN-BINDING PROTEIN 1B | ||||||
![]() | TRANSFERASE / INFECTION / CELL WALL / PEPTIDOGLYCAN / INHIBITOR | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. ...Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C.J. / Dessen, A. | ||||||
![]() | ![]() Title: Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Authors: Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C.J. / Dessen, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 388.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 318 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2y2gC ![]() 2y2hC ![]() 2y2iC ![]() 2y2jC ![]() 2y2kC ![]() 2y2lC ![]() 2y2mC ![]() 2y2nC ![]() 2y2oC ![]() 2y2pC ![]() 2bg1S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.999194, -0.038649, 0.010847), Vector: |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54096.906 Da / Num. of mol.: 2 / Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ALKYL BORONATE (Z06) COVALENTLY BOND TO S460 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases |
---|
-Non-polymers , 6 types, 538 molecules ![](data/chem/img/Z06.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ...ENGINEERED |
---|---|
Nonpolymer details | 3-ACETAMIDO-5-BORONOBENZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.67 Å3/Da / Density % sol: 26.18 % Description: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO 660 |
---|---|
Crystal grow | pH: 7.4 Details: 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→45.6 Å / Num. obs: 76653 / % possible obs: 81.1 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 46.666 Å2 / Rsym value: 0.05 / Net I/σ(I): 30.92 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.97 / Rsym value: 0.49 / % possible all: 53.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BG1 Resolution: 2.15→45.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.702 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.197 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→45.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|