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(-) Description

Title :  CRYSTAL STRUCTURE OF PDZRHOGEF RGRGS DOMAIN IN A COMPLEX WITH GALPHA-13 BOUND TO GDP
 
Authors :  S. R. Sprang, Z. Chen
Date :  23 Apr 08  (Deposition) - 28 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signal Transduction, Protein Complex, Gtp-Binding, Lipoprotein, Membrane, Nucleotide-Binding, Palmitate, Phosphoprotein, Transducer, Coiled Coil, Cytoplasm, Gtpase Activation, Guanine-Nucleotide Releasing Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Chen, W. D. Singer, S. M. Danesh, P. C. Sternweis, S. R. Sprang
Recognition Of The Activated States Of Galpha13 By The Rgrgs Domain Of Pdzrhogef.
Structure V. 16 1532 2008
PubMed-ID: 18940608  |  Reference-DOI: 10.1016/J.STR.2008.07.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-13 SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPFASTBAC
    Expression System Vector TypeVIRUS
    FragmentN-TERMINALLY TRUNCATED
    GeneGNA13, GNA-13
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymG ALPHA-13
 
Molecule 2 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 11
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    FragmentRHOGEF-RGS (RGRGS) DOMAIN
    GeneARHGEF11
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRHOGEF GLUTAMATE TRANSPORT MODULATOR GTRAP48

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , THR A:203 , ASP A:222BINDING SITE FOR RESIDUE MG A 675
2AC2SOFTWAREGLU A:58 , SER A:59 , GLY A:60 , LYS A:61 , SER A:62 , THR A:63 , SER A:173 , LEU A:197 , LEU A:198 , ARG A:200 , ASN A:291 , LYS A:292 , ASP A:294 , LEU A:295 , THR A:348 , ALA A:349 , ILE A:350BINDING SITE FOR RESIDUE GDP A 775

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CX6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CX6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RGSPS50132 RGS domain profile.ARHGB_RAT330-425  1B:330-425

(-) Exons   (0, 0)

(no "Exon" information available for 3CX6)

(-) 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:320
 aligned with GNA13_MOUSE | P27601 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:323
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366   
          GNA13_MOUSE    47 RLVKILLLGAGESGKSTFLKQMRIIHGQDFDQRAREEFRPTIYSNVIKGMRVLVDAREKLHIPWGDNKNQLHGDKLMAFDTRAPMAAQGMVETRVFLQYLPAIRALWEDSGIQNAYDRRREFQLGESVKYFLDNLDKLGVPDYIPSQQDILLARRPTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLEEKVQVVSIKDYFLEFEGDPHCLRDVQKFLVECFRGKRRDQQQRPLYHHFTTAINTENIRLVFRDVKDTILHD 369
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cx6A01 A:47-76,A:203-369     3cx6A02 A:77-202 GI Alpha 1, domain 2-like                                                                                    3cx6A01 A:47-76,A:203-369 P-loop containing nucleotide triphosphate hydrolases                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh......eeeeeeee..eeeeeeee.....hhhhhhhhh....eeeeeee.hhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhh....---...eeee....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cx6 A  47 RLVKILLLGAGESGKSTFLKQMRIIHGQDFDQRAREEFRPTIYSNVIKGMRVLVDAREKLHIPWGDNKNQLHGDKLMAFDTRAPMAAQGMVETRVFLQYLPAIRALWEDSGIQNAYDRRREFQLGESVKYFLDNLDKLGVPDYIPSQQDILLARRPTKGIHEYDFEIKNVPFKMVDVGGLRSERKRWFECFDSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLEEKVQVVSIKDYFLEFEGDPHCLRDVQKFLVECFRGKRRD---RPLYHHFTTAINTENIRLVFRDVKDTILHD 369
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336   |   346       356       366   
                                                                                                                                                                                                                                                                                                                           336 340                             

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with ARHGB_RAT | Q9ES67 from UniProtKB/Swiss-Prot  Length:1527

    Alignment length:196
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496      
            ARHGB_RAT   307 LIIGPEEDYDPGYFNNESDIIFQDLEKLKSHPAYLVVFLRYILSQADPGPLLFYLCSEVYQQTNPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDLRLRNNEDPRNVLCEAQEAVMLEIQEQINDYRSKRTLGLGSLYGENDLLGLDGDPLRERQMAEKQLAALGDILSKYEEDRSAPMDFAVNTFMSHAGI 502
               SCOP domains d3cx6b_          B: automated matches                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...-hhhhhhhhhhhh...........hhhhhhhhhhh-hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------RGS  PDB: B:330-425 UniProt: 330-425                                                            ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cx6 B 307 LIIGPEE---------ESDIIFQDLEKLKSHPAYLVVFLRYILSQADPGPLLFYLCSEVYQQTNPK-SRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDLR-RNNEDPRNVLCEAQEAVMLEIQEQINDYRSKRTLGLGSLYGENDLLGLDGDPLRERQMAEKQLAALGDILSKYEEDRSAPMDFAVNTFMSHAGI 502
                                  |  -      |326       336       346       356       366     | 376       386       396       406| |    416       426       436       446       456       466       476       486       496      
                                313       323                                              372 |                              407 |                                                                                             
                                                                                             374                                409                                                                                             

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CX6)

(-) Gene Ontology  (42, 48)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GNA13_MOUSE | P27601)
molecular function
    GO:0031752    D5 dopamine receptor binding    Interacting selectively and non-covalently with a D5 dopamine receptor.
    GO:0031683    G-protein beta/gamma-subunit complex binding    Interacting selectively and non-covalently with a complex of G-protein beta/gamma subunits.
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    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:0019001    guanyl nucleotide binding    Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0031702    type 1 angiotensin receptor binding    Interacting selectively and non-covalently with a type 1 angiotensin receptor.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007266    Rho protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
    GO:0031584    activation of phospholipase D activity    Any process that initiates the activity of inactive phospholipase D.
    GO:0007189    adenylate cyclase-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP).
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0001569    branching involved in blood vessel morphogenesis    The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005834    heterotrimeric G-protein complex    Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (ARHGB_RAT | Q9ES67)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007266    Rho protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0001505    regulation of neurotransmitter levels    Any process that modulates levels of neurotransmitter.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHGB_RAT | Q9ES673cx7 3cx8
        GNA13_MOUSE | P276011shz 1zcb 3ab3 3cx7 3cx8

(-) Related Entries Specified in the PDB File

1shz CRYSTAL STRUCTURE OF THE P115RHOGEF RGRGS DOMAIN IN A COMPLEX WITH GALPHA(13):GALPHA(I1) CHIMERA
3cx7 CRYSTAL STRUCTURE OF PDZRHOGEF RGRGS DOMAIN IN A COMPLEX WITH GALPHA-13 BOUND TO GDP-ALF4
3cx8 CRYSTAL STRUCTURE OF PDZRHOGEF RGRGS DOMAIN IN A COMPLEX WITH GALPHA-13 BOUND TO GTP-GAMMA-S