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Sandbox Reserved 1474

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{{Structure
{{Structure
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|PDB= {{{3GKZ}}}|SCENE={{{SCENE|}}}|SIZE={{{SIZE|350}}}|CAPTION={{{CAPTION|[[3GKZ]], [[Resolution|resolution]] 1.90Å ; (<scene name='3gkz'>default scene</scene>)}}}
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|PDB= {{{4LAR}}}|SCENE={{{SCENE|}}}|SIZE={{{SIZE|350}}}|CAPTION={{{CAPTION|[[Crystal structures of a therapeutic single chain antibody in the free Form and in complex with amphetamine]], [[Resolution|resolution]] 2.38&Aring; (<scene name='4LAR'>default scene</scene>)}}}
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|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=P3S:L-METHIONINE-S-SULFOXIMINE+PHOSPHATE'>P3S</scene>
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|LIGAND= <scene name='pdbligand=1WE:(2S)-1-PHENYLPROPAN-2-AMINE'>AMP</scene>,
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--ammonia_ligase Glutamate--ammonia ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.1.2 6.3.1.2] </span>
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|ACTIVITY= <span class='plainlinks'>[], </span>
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|GENE= GLUL, GLNS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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|GENE= )
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|RELATEDENTRY=[[2ojw|2ojw]]
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|RELATEDENTRY=[[3gkz|3gkz]], [[4laq|4laq]], [[4las|4las]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc8 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc8 PDBsum]</span>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lar OCA], [http://pdbe.org/4lar PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lar RCSB], [http://www.ebi.ac.uk/pdbsum/4lar PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lar ProSAT]</span>
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|FUNCTION={{GO|id=GO:0016874 | text = ligase activity}}{{GO|id=GO:0004356 | text = glutamate-ammonia ligase activity}}{{GO|id=GO:0003824 | text = catalytic activity}}
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|FUNCTION={{GO|id=GO: | text = }}{{GO|id=GO: | text = }}{{GO|id=GO: | text = }}
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|PROCESS={{GO|id=GO:0006807 | text = nitrogen compound metabolic process}}{{GO|id=GO:0006542 | text = glutamine biosynthetic process}}{{GO|id=GO:0001505 | text = regulation of neurotransmitter levels}}
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|PROCESS={{GO|id=GO: | text = }}{{GO|id=GO: | text = }}{{GO|id=GO: | text = }}
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|COMPONENT={{GO|id=GO:0005737 | text = cytoplasm}}
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|COMPONENT={{GO|id=GO: | text = }}
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|SARESOURCES=<span class='plainlinks'>InterPro : [http://www.ebi.ac.uk/interpro/ISearch?query=IPR014746 Ipr014746], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR008147 Ipr008147], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR008146 Ipr008146]<br>Pfam : [http://pfam.sanger.ac.uk/family?acc=PF00120 PF00120], [http://pfam.sanger.ac.uk/family?acc=PF03951 PF03951]<br>UniProt : [http://ca.expasy.org/cgi-bin/niceprot.pl?P15104 P15104]</span>
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|uPDB=2QC8|CONSURF={{!}}-
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{{!}} colspan="2" style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;" {{!}} [[Image:Consurf_key_small.gif|center]]
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{{!}}-{{!}} style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"
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{{!}} '''Toggle Conservation Colors:'''
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{{!}} align="left" style="background-color:#acfaac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" {{!}}
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Rows = identical sequences:
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<jmol>
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<jmolButton>
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<script></script>
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<text>A [x]</text>
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<name>jmb_2qc8_A</name>
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<title>toggle chain A</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>B [x]</text>
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<name>jmb_2qc8_B</name>
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<title>toggle chain B</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>C [x]</text>
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<name>jmb_2qc8_C</name>
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<title>toggle chain C</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>D [x]</text>
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<name>jmb_2qc8_D</name>
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<title>toggle chain D</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>E [x]</text>
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<name>jmb_2qc8_E</name>
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<title>toggle chain E</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>F [x]</text>
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<name>jmb_2qc8_F</name>
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<title>toggle chain F</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>G [x]</text>
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<name>jmb_2qc8_G</name>
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<title>toggle chain G</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>H [x]</text>
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<name>jmb_2qc8_H</name>
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<title>toggle chain H</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>I [x]</text>
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<name>jmb_2qc8_I</name>
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<title>toggle chain I</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script></script>
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<text>J [x]</text>
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<name>jmb_2qc8_J</name>
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<title>toggle chain J</title>
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<jsscript>ConsurfChainButton(elementClicked)</jsscript>
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<appendtargetsuffixtoid>true</appendtargetsuffixtoid>
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</jmolButton>
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</jmol>
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}}
}}

Revision as of 07:57, 7 December 2018

Contents

Introduction

==================================

Drag the structure with the mouse to rotate
Crystal structures of a therapeutic single chain antibody in the free Form and in complex with amphetamine, resolution 2.38Å ()
Ligands: ,
Gene: )
Activity: [],
Related: 3gkz, 4laq, 4las
Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
Coordinates: save as pdb, mmCIF, xml



==================================

4LAQ

Drag the structure with the mouse to rotate

, , , ,


3GKZ

Drag the structure with the mouse to rotate

Scene 3GKZ hydrophobic interaction between ligand and residues on LDRs Scene 3GKZ cationic Nitrogen with residual hydrogen bonds Scene 3GKZ solevent hydrogen bonds stabilizing the binding

Scene 4LAR Scene 4LAS

You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.

Function

Disease

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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