[English] 日本語
![](img/lk-miru.gif)
- PDB-4re5: Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4re5 | ||||||
---|---|---|---|---|---|---|---|
Title | Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor | ||||||
![]() | Acylamino-acid-releasing enzyme![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Menyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V. | ||||||
![]() | ![]() Title: Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. Authors: Menyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 451.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 370 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4re6C ![]() 2hu5S 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: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 8 - 581 / Label seq-ID: 8 - 581
| ||||||||||||||||||
Details | The biological assembly is dimer consisting of chains A and B of the asymmetric unit. |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 63108.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: APE_1547.1 / Plasmid: pET22b / Production host: ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 669 molecules ![](data/chem/img/Y3A.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() ![]() ![]() Details: The chlorormethyl ketone inhibitor linked to the protein through two covalent bonds with the active site serine and histidine References: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) #3: Chemical | ChemComp-ACT / | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-CL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 78 mM sodium acetate buffer, 2.4% w/v PEG Mw4000, 6.7mM dithiothreitol and 0.44 mM EDTA. The protein was co-crystallized with the inhibitor., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2010 / Details: mirrors (Blue) |
Radiation | Monochromator: Rigaku confocal Blue optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→20 Å / Num. all: 90022 / Num. obs: 90022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Biso Wilson estimate: 32.79 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.58 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6591 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2HU5 Resolution: 1.9→19.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.984 / SU ML: 0.117 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 35.253 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|