[English] 日本語
![](img/lk-miru.gif)
- PDB-2r5d: Structure of the gp41 N-trimer in complex with the HIV entry inhi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2r5d | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the gp41 N-trimer in complex with the HIV entry inhibitor PIE7 | ||||||
![]() |
| ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / HIV ENTRY INHIBITOR PIE7 / polypeptide(D) / polypeptide(D) (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() | ||||||
![]() | VanDemark, A.P. / Welch, B. / Heroux, A. / Hill, C.P. / Kay, M.S. | ||||||
![]() | ![]() Title: Potent D-peptide inhibitors of HIV-1 entry Authors: Welch, B.D. / Vandemark, A.P. / Heroux, A. / Hill, C.P. / Kay, M.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein/peptide / Polypeptide(D) , 2 types, 6 molecules ABCHKL
#1: Protein/peptide | Mass: 5466.574 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others) #2: Polypeptide(D) | |
---|
-Non-polymers , 4 types, 189 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / ![]() |
---|---|
#4: Chemical | ChemComp-SO4 / ![]() |
#5: Chemical | ChemComp-EPE / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES, 24% PEG 10000, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→50 Å / Num. all: 24829 / Num. obs: 23406 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.046 / Χ2: 1.625 / Net I/σ(I): 21.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.66→38.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.434 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.122 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.427 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→38.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
|