Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF IGLUR5 LIGAND-BINDING CORE (S1S2) IN COMPLEX WITH DYSIHERBAINE AT 1.35A RESOLUTION
 
Authors :  K. Frydenvang, P. Naur, M. Gajhede, J. S. Kastrup
Date :  19 Feb 09  (Deposition) - 17 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ionotropic Glutamate Receptors, Iglur5, Ligand-Binding Core, Agonist, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Frydenvang, L. L. Lash, P. Naur, P. A. Postila, D. S. Pickering, C. M. Smith, M. Gajhede, M. Sasaki, R. Sakai, O. T. Pentikainen, G. T. Swanson, J. S. Kastrup
Full Domain Closure Of The Ligand-Binding Core Of The Ionotropic Glutamate Receptor Iglur5 Induced By The High Affinity Agonist Dysiherbaine And The Functional Antagonist 8, 9-Dideoxyneodysiherbaine
J. Biol. Chem. V. 284 14219 2009
PubMed-ID: 19297335  |  Reference-DOI: 10.1074/JBC.M808547200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A(+)
    Expression System StrainORIGAMI 2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentIGLUR5 LIGAND-BINDING CORE (S1S2)
    GeneGLUR5, GRIK1
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGLUTAMATE RECEPTOR 5, GLUR-5, GLUR5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DYH4Ligand/Ion(2R,3AR,6S,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6-HYDROXY-7-(METHYLAMINO)HEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC ACID
3GOL3Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DYH1Ligand/Ion(2R,3AR,6S,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6-HYDROXY-7-(METHYLAMINO)HEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC ACID
3GOL1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DYH1Ligand/Ion(2R,3AR,6S,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6-HYDROXY-7-(METHYLAMINO)HEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC ACID
3GOL1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DYH1Ligand/Ion(2R,3AR,6S,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6-HYDROXY-7-(METHYLAMINO)HEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC ACID
3GOL1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DYH1Ligand/Ion(2R,3AR,6S,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6-HYDROXY-7-(METHYLAMINO)HEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 3GBA)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:202 -A:256
2B:202 -B:256
3C:202 -C:256
4D:202 -D:256

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:14 -Pro A:15
2Glu B:14 -Pro B:15
3Glu C:14 -Pro C:15
4Glu D:14 -Pro D:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GBA)

(-) Exons   (0, 0)

(no "Exon" information available for 3GBA)

(-) Sequences/Alignments

Asymmetric 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:257
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:389
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811         
            GRIK1_RAT   432 GNRDRSNNITDSLANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 820
               SCOP domains d            3gbaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3            gbaA01 A:1-108,A:214-257 Periplasmic binding protein-like II                                               ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gbaA01 A:1-108,A:214-257                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gba A   1 G------------ANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 257
                            |        -   |     8        18        28        38        48        58        68        78        88        98       108       | -||       -         -         -         -         -         -         -         -         -         -         -         -|      128       138       148       158       168       178       188       198       208       218       228       238       248         
                            |            2                                                                                                               116  ||                                                                                                                    119                                                                                                                                          
                            1                                                                                                                               117|                                                                                                                                                                                                                                                                 
                                                                                                                                                             118                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:389
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811         
            GRIK1_RAT   432 GNRDRSNNITDSLANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 820
               SCOP domains d            3gbab_ B: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3            gbaB01 B:1-108,B:213-257 Periplasmic binding protein-like II                                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gbaB01 B:1-108,B:213-257                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh....eeeee..hhhhhhhhhh.hhhhhhhhhhhh......ee.hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gba B   1 G------------ANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 257
                            |        -   |     8        18        28        38        48        58        68        78        88        98       108       | -||       -         -         -         -         -         -         -         -         -         -         -         -|      128       138       148       158       168       178       188       198       208       218       228       238       248         
                            1            2                                                                                                               116  ||                                                                                                                    119                                                                                                                                          
                                                                                                                                                            117|                                                                                                                                                                                                                                                                 
                                                                                                                                                             118                                                                                                                                                                                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:251
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:373
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817   
            GRIK1_RAT   448 TLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 820
               SCOP domains d3gbac_ C: automated matches                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gbaC01 C:5-108,C:214-257 Periplasmic binding protein-like II                                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gbaC01 C:5-108,C:214-257                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh..ee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh.-..eee....hhhhhhhhhh.hhhhhhhhhhhh..-......hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gba C   5 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQ-KIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSR-QSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 257
                                    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   
                                                                                                                                         116  ||                                                                                                                    119       129 |                              164 |                                                                                           
                                                                                                                                            117|                                                                                                                                131                                166                                                                                           
                                                                                                                                             118                                                                                                                                                                                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:250
 aligned with GRIK1_RAT | P22756 from UniProtKB/Swiss-Prot  Length:949

    Alignment length:373
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817   
            GRIK1_RAT   448 TLIVTTILEEPYVMYRKSDKPLYGNDRFEAYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFTPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 820
               SCOP domains d3gbad_ D: automate d matches                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gbaD01 D:5-108,D:2 14-257 Periplasmic binding protein-like II                                          --------  --                                                                                                                      ----------- ---------------------------------- ------------------------------------------------3gbaD01 D:5-108,D:214-257                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee....-..hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh..ee....eee.eeeeee.--..----------------------------------------------------------------------------------------------------------------------...hhhhhhh.-..eee....hhhhhhhhhh.hhhhhhhhhhhh..-......hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gba D   5 TLIVTTILEEPYVMYRKSD-PLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRK--GT----------------------------------------------------------------------------------------------------------------------PIDSADDLAKQ-KIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSR-QSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 257
                                    14        |-|       34        44        54        64        74        84        94       104       114 |  ||   -         -         -         -         -         -         -         -         -         -         -         -    |  124    | |134       144       154       164 |     174       184       194       204       214       224       234       244       254   
                                             23 |                                                                                        116  ||                                                                                                                    119       129 |                              164 |                                                                                           
                                               25                                                                                           117|                                                                                                                                131                                166                                                                                           
                                                                                                                                             118                                                                                                                                                                                                                                                                 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GRIK1_RAT | P22756)
molecular function
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0005234    extracellular-glutamate-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0016595    glutamate binding    Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0015277    kainate selective glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate, acts by opening a cation channel permeable to sodium and potassium, and for which kainate is an agonist.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0022843    voltage-gated cation channel activity    Enables the transmembrane transfer of a cation by a voltage-gated channel. A cation is a positively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0032229    negative regulation of synaptic transmission, GABAergic    Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    GO:0051967    negative regulation of synaptic transmission, glutamatergic    Any process that stops, prevents, or reduces the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0032230    positive regulation of synaptic transmission, GABAergic    Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0048172    regulation of short-term neuronal synaptic plasticity    A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DYH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3gba)
 
  Cis Peptide Bonds
    Glu A:14 - Pro A:15   [ RasMol ]  
    Glu B:14 - Pro B:15   [ RasMol ]  
    Glu C:14 - Pro C:15   [ RasMol ]  
    Glu D:14 - Pro D:15   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3gba
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GRIK1_RAT | P22756
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GRIK1_RAT | P22756
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GRIK1_RAT | P227561txf 1vso 1ycj 2f34 2f35 2f36 2ojt 2pbw 2qs1 2qs2 2qs3 2qs4 2wky 3c31 3c32 3c33 3c34 3c35 3c36 3gbb 3s2v 4dld 4e0x 4qf9 4ymb 5m2v 5mfq 5mfv 5mfw

(-) Related Entries Specified in the PDB File

1ycj X-RAY STRUCTURE OF IGLUR5 LIGAND-BINDING CORE WITH L- GLUTAMATE
3gbb