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Yorodumi- PDB-2l87: The 27-residue N-terminus CCR5-peptide in a ternary complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l87 | ||||||
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Title | The 27-residue N-terminus CCR5-peptide in a ternary complex with HIV-1 gp120 and a CD4-mimic peptide | ||||||
Components | C-C chemokine receptor type 5 | ||||||
Keywords | SIGNALING PROTEIN / helix / HIV co-receptor | ||||||
Function / homology | Function and homology information chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Schnur, E. / Noah, E. / Ayzenshtat, I. / Sargsyan, H. / Inui, T. / Ding, F.X. / Arshava, B. / Sagi, Y. / Kessler, N. / Levy, R. ...Schnur, E. / Noah, E. / Ayzenshtat, I. / Sargsyan, H. / Inui, T. / Ding, F.X. / Arshava, B. / Sagi, Y. / Kessler, N. / Levy, R. / Scherf, T. / Naider, F. / Anglister, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Conformation and Orientation of a 27-Residue CCR5 Peptide in a Ternary Complex with HIV-1 gp120 and a CD4-Mimic Peptide. Authors: Schnur, E. / Noah, E. / Ayzenshtat, I. / Sargsyan, H. / Inui, T. / Ding, F.X. / Arshava, B. / Sagi, Y. / Kessler, N. / Levy, R. / Scherf, T. / Naider, F. / Anglister, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l87.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l87.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 2l87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/2l87 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/2l87 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3357.653 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-27 / Mutation: C20A / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Contents: 1mM Nt-CCR5; 0.1mM gp120/CD4mimic; 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: 300 / pH: 7.0 / Temperature units: K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1 |