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(-) Description

Title :  THE CRYSTAL STRUCTURE OF GTR1P-GTR2P COMPLEXED WITH GTP-GDP
 
Authors :  J. H. Jeong, Y. G. Kim
Date :  27 Apr 12  (Deposition) - 25 Jul 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Gtpase, Cell Growth (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Jeong, K. H. Lee, Y. M. Kim, D. H. Kim, B. H. Oh, Y. G. Kim
Crystal Structure Of The Gtr1Pgtp-Gtr2Pgdp Complex Reveals Large Structural Rearrangements Triggered By Gtp-To-Gdp Conversion
J. Biol. Chem. V. 287 29648 2012
PubMed-ID: 22807443  |  Reference-DOI: 10.1074/JBC.C112.384420

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN GTR1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPPROEXHTA
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
 
Molecule 2 - GTP-BINDING PROTEIN GTR2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPPROEXHTA
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:15 , GLY A:16 , SER A:17 , GLY A:18 , LYS A:19 , SER A:20 , SER A:21 , ALA A:40 , THR A:41 , GLY A:63 , GLY A:64 , HIS A:126 , LYS A:127 , ASP A:129 , LEU A:130 , SER A:165 , ILE A:166 , MG A:500BINDING SITE FOR RESIDUE GTP A 400
2AC2SOFTWARESER A:20 , THR A:41 , GTP A:400BINDING SITE FOR RESIDUE MG A 500
3AC3SOFTWAREARG B:19 , CYS B:20 , GLY B:21 , LYS B:22 , SER B:23 , SER B:24 , HIS B:124 , LYS B:125 , ASP B:127 , SER B:165 , ILE B:166 , PHE B:167BINDING SITE FOR RESIDUE GDP B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ARZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ARZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ARZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ARZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4ARZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:291
 aligned with GTR1_YEAST | Q00582 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
           GTR1_YEAST     4 NNRKKLLLMGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLGNMTLNLWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSEFGFPNLIGFPTSIWDESLYKAWSQIVCSLIPNMSNHQSNLKKFKEIMNALEIILFERTTFLVICSSNGENSNENHDSSDNNNVLLDPKRFEKISNIMKNFKQSCTKLKSGFKTLILNNNIYVSELSSNMVCFIVLKDMNIPQELVLENIKKAKEFFQ 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhh...hhhhhhhh....eeeeeeee...eeeeeeee..hhhhhhhhhh.hhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeeee.....eeeee.----------------....hhhhhhhhhhhhhhh........eeeeee...eeeee....eeeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4arz A   4 NNRKKLLLMGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLGNMTLNLWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSEFGFPNLIGFPTSIWDESLYKAWSQIVCSLIPNMSNHQSNLKKFKEIMNALEIILFERTTFLVICSSN----------------LLDPKRFEKISNIMKNFKQSCTKLKSGFKTLILNNNIYVSELSSNMVCFIVLKDMNIPQELVLENIKKAKEFFQ 310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      |  -         -   |   243       253       263       273       283       293       303       
                                                                                                                                                                                                                                                  220              237                                                                         

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with GTR2_YEAST | P53290 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:321
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324 
           GTR2_YEAST     5 ATDSKAMVLLMGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHFSTLIDLAVMELPGQLNYFEPSYDSERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPSINIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLELGLDGVQVSFYLTSIFDHSIYEAFSRIVQKLIPELSFLENMLDNLIQHSKIEKAFLFDVNSKIYVSTDSNPVDIQMYEVCSEFIDVTIDLFDLYKAPVLRNSQKSSDKDNVINPRNELQNVSQLANGVIIYLRQMIRGLALVAIIRPNGTDMESCLTVADYNIDIFKKGLEDIW 325
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhhhhhhhhh....hhhhh.......eeeee.........hhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.......ee........hhhhhhhhhhhhhhhhhhhh.-----------------.....eeeeee....eeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4arz B   5 ATDSKAMVLLMGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHFSTLIDLAVMELPGQLNYFEPSYDSERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPSINIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLELGLDGVQVSFYLTSIFDHSIYEAFSRIVQKLIPELSFLENMLDNLIQHSKIEKAFLFDVNSKIYVSTDSNPVDIQMYEVCSEFIDVTIDLFDLYKA-----------------PRNELQNVSQLANGVIIYLRQMIRGLALVAIIRPNGTDMESCLTVADYNIDIFKKGLEDIW 325
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  |      -         -|      274       284       294       304       314       324 
                                                                                                                                                                                                                                                                            247               265                                                            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ARZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ARZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ARZ)

(-) Gene Ontology  (31, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GTR1_YEAST | Q00582)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1904263    positive regulation of TORC1 signaling    Any process that activates or increases the frequency, rate or extent of TORC1 signaling.
    GO:1903778    protein localization to vacuolar membrane    A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006360    transcription from RNA polymerase I promoter    The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
    GO:0006383    transcription from RNA polymerase III promoter    The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0034448    EGO complex    A vacuolar membrane-associated protein complex that is required for activation of microautophagy during exit from rapamycin-induced growth arrest. In budding yeast, S. cerevisiae, this complex includes Gtr1p, Gtr2p, Meh1p, and Slm4p.
    GO:1990131    Gtr1-Gtr2 GTPase complex    A heterodimer GTPase complex. In S. cerevisiae, this complex contains Gtr1p and Gtr2p proteins.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Chain B   (GTR2_YEAST | P53290)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0016237    lysosomal microautophagy    The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1904263    positive regulation of TORC1 signaling    Any process that activates or increases the frequency, rate or extent of TORC1 signaling.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1903778    protein localization to vacuolar membrane    A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0034448    EGO complex    A vacuolar membrane-associated protein complex that is required for activation of microautophagy during exit from rapamycin-induced growth arrest. In budding yeast, S. cerevisiae, this complex includes Gtr1p, Gtr2p, Meh1p, and Slm4p.
    GO:1990131    Gtr1-Gtr2 GTPase complex    A heterodimer GTPase complex. In S. cerevisiae, this complex contains Gtr1p and Gtr2p proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GTR1_YEAST | Q005823r7w
        GTR2_YEAST | P532903r7w

(-) Related Entries Specified in the PDB File

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