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Yorodumi- PDB-1czq: CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1czq | ||||||
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Title | CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET. | ||||||
Components |
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Keywords | Viral protein/inhibitor / ENVELOPE GLYCOPROTEIN / Viral protein-inhibitor COMPLEX | ||||||
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 / : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Human immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Eckert, D.M. / Malashkevich, V.N. / Hong, L.H. / Carr, P.A. / Kim, P.S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Inhibiting HIV-1 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: Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of GCN4-pIQI, a trimeric coiled-coil with buried polar residues. #2: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Core structure of gp41 from the HIV envelope glycoprotein | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1czq.cif.gz | 25.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1czq.ent.gz | 20.3 KB | Display | PDB format |
PDBx/mmJSON format | 1czq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1czq ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1czq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 5468.566 Da / Num. of mol.: 1 / Fragment: HYDROPHOBIC POCKET Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae, Human immunodeficiency virus Genus: Saccharomyces, Lentivirus / Species: , / Strain: , / References: GenBank: 1587615 |
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#2: Protein/peptide | Mass: 1859.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% PEG 4000 0.1 M SODIUM CITRATE 20% 2-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1197, 1.1393, 1.1403, 1.1399 | |||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 24, 1999 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→35 Å / Num. all: 14503 / Num. obs: 13604 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.8 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.5 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Resolution: 1.5→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 646169.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.34 Å2 / ksol: 0.394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.233 |