[English] 日本語
![](img/lk-miru.gif)
- PDB-6gz9: Crystal structure of a POT family transporter in complex with pro... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6gz9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a POT family transporter in complex with prodrug valacyclovir | ||||||
![]() | Peptide ABC transporter permease | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() peptide transport / peptide transmembrane transporter activity / membrane => GO:0016020 / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minhas, G.S. / Newstead, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters. Authors: Minhas, G.S. / Newstead, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6h7uC ![]() 6hzpC ![]() 6exsS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53951.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-TXC / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.33 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 26-27% (v/v) PEG 200, 220 mM (NH4)2HPO4, and 110 mM sodium citrate (pH 5.0). Ligand: 40mM valacyclovir |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.1→58.2 Å / Num. obs: 11917 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 60.92 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.23 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.17 / Num. unique obs: 2145 / CC1/2: 0.547 / Rpim(I) all: 0.94 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 6EXS Resolution: 3.1→58.162 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.76
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.79 Å2 / Biso mean: 69.1491 Å2 / Biso min: 33.95 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→58.162 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
|