+
Open data
-
Basic information
Entry | Database: PDB / ID: 3l35 | ||||||
---|---|---|---|---|---|---|---|
Title | PIE12 D-peptide against HIV entry | ||||||
![]() |
| ||||||
![]() | ![]() ![]() | ||||||
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![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Welch, B.D. / Redman, J.S. / Paul, S. / Whitby, F.G. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S. | ||||||
![]() | ![]() Title: Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance. Authors: Welch, B.D. / Francis, J.N. / Redman, J.S. / Paul, S. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Whitby, F.G. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 10560 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 10620 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, B, C, H, K, L BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
-
Components
#1: Protein/peptide | Mass: 5466.574 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: L-PEPTIDE WITH N-TERMINAL ACETYL GROUP AND C-TERMINAL AMIDE GROUP #2: Protein/peptide | Mass: 2029.301 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: D-PEPTIDE WITH N-TERMINAL ACETYL GROUP AND C-TERMINAL AMIDE GROUP #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
---|---|
Crystal grow![]() | pH: 9 Details: 0.1 M BICINE, 2% V/V 1,4-DIOXANE, 10% W/V POLYETHYLENE GLYCOL 20,000, PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 2008 / Details: VARIMAX-HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→30 Å / Num. obs: 25088 / % possible obs: 86.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.669 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / % possible all: 66.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.98 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|