+
Open data
-
Basic information
Entry | Database: PDB / ID: 2q5u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of IQN17 | ||||||
![]() | Fusion protein between yeast variant GCN4 and HIVgp41 | ||||||
![]() | VIRAL PROTEIN / envelope glycoprotein / coiled coil / viral protein/viral protein inhibitor | ||||||
Function / homology | ![]() positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malashkevich, V.N. / Eckert, D.M. / Hong, L.H. / Kim, P.S. | ||||||
![]() | ![]() Title: Inhibiting HIV Entry: Discovery of D-Peptide Inhibitors that Target the Gp41 Coiled-Coil Pocket Authors: Eckert, D.M. / Malashkevich, V.N. / Hong, L.H. / Carr, P.A. / Kim, P.S. #1: ![]() Title: Crystal Structure of GCN4-Piqi, a Trimeric Coiled-Coil with Buried Polar Residues. Authors: Eckert, D.M. / Malashkevich, V.N. / Kim, P.S. #2: ![]() Title: Core structure of gp41 from the HIV envelope glycoprotein Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 44.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 32.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1czqSC ![]() 2q3iC ![]() 2q7cC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Unit cell contains biological assembly, trimer |
-
Components
#1: Protein/peptide | Mass: 5468.566 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Synthetic Peptide. The sequence naturally occurs in Saccharomyces cerevisiae and human immunodeficiency virus. References: UniProt: A3F986 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.84 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 21% PEG4000, 0.15 M ammonium sulfate, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2000 / Details: X4A |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 24434 / Num. obs: 24434 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2221 / Rsym value: 0.32 / % possible all: 95.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 1CZQ Resolution: 1.5→18.69 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.855 / SU B: 1.603 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.119 / 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: 21.688 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→18.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.499→1.537 Å / Total num. of bins used: 20
|