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- PDB-2bgr: Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) boun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bgr | |||||||||
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Title | Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26) | |||||||||
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![]() | HYDROLASE / HYDROLASE-COMPLEX / DPPIV / ALPHA/BETA-HYDROLASE FOLD / BETA-PROPELLER FOLD | |||||||||
Function / homology | ![]() viral gene expression / trans-activation response element binding / regulatory region RNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / glucagon processing / modulation by virus of host chromatin organization / negative regulation of neutrophil chemotaxis / symbiont-mediated suppression of host translation initiation / regulation of cell-cell adhesion mediated by integrin ...viral gene expression / trans-activation response element binding / regulatory region RNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / glucagon processing / modulation by virus of host chromatin organization / negative regulation of neutrophil chemotaxis / symbiont-mediated suppression of host translation initiation / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / host cell nucleolus / intercellular canaliculus / chemorepellent activity / actinin binding / dipeptidyl-peptidase activity / peptide hormone processing / negative regulation of peptidyl-threonine phosphorylation / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / RNA-binding transcription regulator activity / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / host cell cytoplasm / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / membrane raft / apical plasma membrane / protein domain specific binding / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / DNA-templated transcription / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Weihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H. | |||||||||
![]() | ![]() Title: Crystal Structures of HIV-1 Tat-Derived Nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase Iv (Cd26) Authors: Weihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 352.2 KB | Display | ![]() |
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PDB format | ![]() | 284.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bgnC ![]() 1n1mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6
NCS oper: (Code: given Matrix: (-0.946, 0.152, -0.287), Vector: |
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Components
-Protein / Protein/peptide / Non-polymers , 3 types, 1750 molecules ABYZ![](data/chem/img/HOH.gif)
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#1: Protein | Mass: 85452.570 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 29-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1029.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #8: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 14 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.56 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 127470 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 87.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N1M Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.392 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 29 - 37 ARE DISORDERED AND WERE NOT MODELLED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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