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(-) Description

Title :  STRUCTURE OF THE METHUSELAH ECTODOMAIN WITH PEPTIDE INHIBITOR
 
Authors :  A. P. West Jr. , W. W. Ja, S. L. Delker, P. J. Bjorkman, S. Benzer, R. W. Roberts
Date :  18 May 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
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 :  Gpcr G Protein-Coupled Receptor Ectodomain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. W. Ja, A. P. West, S. L. Delker, P. J. Bjorkman, S. Benzer, R. W. Roberts
Extension Of Drosophila Melanogaster Life Span With A Gpcr Peptide Inhibitor.
Nat. Chem. Biol. V. 3 415 2007
PubMed-ID: 17546039  |  Reference-DOI: 10.1038/NCHEMBIO.2007.2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - G-PROTEIN COUPLED RECEPTOR MTH
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    FragmentN-TERMINAL EXTRACELLULAR DOMAIN
    GeneMTH
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymPROTEIN METHUSELAH

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PZX)

(-) Sites  (0, 0)

(no "Site" information available for 2PZX)

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:5 -A:59
2A:61 -A:66
3A:70 -A:164
4A:71 -A:82
5A:126 -A:185
6B:5 -B:59
7B:61 -B:66
8B:70 -B:164
9B:71 -B:82
10B:126 -B:185
11C:5 -C:59
12C:61 -C:66
13C:70 -C:164
14C:71 -C:82
15C:126 -C:185
16D:5 -D:59
17D:61 -D:66
18D:70 -D:164
19D:71 -D:82
20D:126 -D:185

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PZX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 12)

Asymmetric Unit (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTH_DROME_001 *L54IMTH_DROME  ---  ---A/B/C/DL30I
2UniProtVAR_MTH_DROME_002 *S132AMTH_DROME  ---  ---A/B/C/DS108A
3UniProtVAR_MTH_DROME_003 *D151NMTH_DROME  ---  ---A/B/C/DD127N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTH_DROME_001 *L54IMTH_DROME  ---  ---AL30I
2UniProtVAR_MTH_DROME_002 *S132AMTH_DROME  ---  ---AS108A
3UniProtVAR_MTH_DROME_003 *D151NMTH_DROME  ---  ---AD127N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTH_DROME_001 *L54IMTH_DROME  ---  ---BL30I
2UniProtVAR_MTH_DROME_002 *S132AMTH_DROME  ---  ---BS108A
3UniProtVAR_MTH_DROME_003 *D151NMTH_DROME  ---  ---BD127N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTH_DROME_001 *L54IMTH_DROME  ---  ---CL30I
2UniProtVAR_MTH_DROME_002 *S132AMTH_DROME  ---  ---CS108A
3UniProtVAR_MTH_DROME_003 *D151NMTH_DROME  ---  ---CD127N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTH_DROME_001 *L54IMTH_DROME  ---  ---DL30I
2UniProtVAR_MTH_DROME_002 *S132AMTH_DROME  ---  ---DS108A
3UniProtVAR_MTH_DROME_003 *D151NMTH_DROME  ---  ---DD127N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PZX)

(-) Exons   (0, 0)

(no "Exon" information available for 2PZX)

(-) 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:188
 aligned with MTH_DROME | O97148 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:188
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
            MTH_DROME    25 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 212
               SCOP domains d2pzxa1 A:1-188 Methuselah ectodomain                                                                                                                                                        SCOP domains
               CATH domains 2pzxA01 A:1-63  [code=2.30.160.11, no name defined]            2pzxA02 A:64-188 Methuselah ectodomain, domain 2                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhee....ee.....eee..eeehhh.eeeeeeee.....eeeeeeeeee.hhhh..eee.......eee..eee...hhhhhh.ee.eeeee.....eeeee.....eee..........ee....hhhh.eeee....eee....eee....eeeeeee........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------I-----------------------------------------------------------------------------A------------------N------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzx A   1 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with MTH_DROME | O97148 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:188
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
            MTH_DROME    25 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 212
               SCOP domains d2pzxb1 B:1-188 Methuselah ectodomain                                                                                                                                                        SCOP domains
               CATH domains 2pzxB01 B:1-63  [code=2.30.160.11, no name defined]            2pzxB02 B:64-188 Methuselah ectodomain, domain 2                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhee....ee.....eee..eeehhh.eeeeeeee.....eeeeeeeeee.hhhh..eee.......eee..eee...hhhhhh.ee.eeeee.....eeeee.....eee..........ee....hhhh.eeee....eee....eee....eeeeeee........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------I-----------------------------------------------------------------------------A------------------N------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzx B   1 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        

Chain C from PDB  Type:PROTEIN  Length:188
 aligned with MTH_DROME | O97148 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:188
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
            MTH_DROME    25 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 212
               SCOP domains d2pzxc1 C:1-188 Methuselah ectodomain                                                                                                                                                        SCOP domains
               CATH domains 2pzxC01 C:1-63  [code=2.30.160.11, no name defined]            2pzxC02 C:64-188 Methuselah ectodomain, domain 2                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhee....ee.....eee..eeehhh.eeeeeeee.....eeeeeeeeee.hhhh..eee.......eee..eee...hhhhhh.ee.eeeee.....eeeee.....eee..........ee....hhhh.eeee....eee....eee....eeeeeee........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------I-----------------------------------------------------------------------------A------------------N------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzx C   1 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        

Chain D from PDB  Type:PROTEIN  Length:188
 aligned with MTH_DROME | O97148 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:188
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
            MTH_DROME    25 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 212
               SCOP domains d2pzxd1 D:1-188 Methuselah ectodomain                                                                                                                                                        SCOP domains
               CATH domains 2pzxD01 D:1-63  [code=2.30.160.11, no name defined]            2pzxD02 D:64-188 Methuselah ectodomain, domain 2                                                                              CATH domains
           Pfam domains (1) ----Methuselah_N-2pzxD01 D:5-185                                                                                                                                                         --- Pfam domains (1)
           Pfam domains (2) ----Methuselah_N-2pzxD02 D:5-185                                                                                                                                                         --- Pfam domains (2)
           Pfam domains (3) ----Methuselah_N-2pzxD03 D:5-185                                                                                                                                                         --- Pfam domains (3)
           Pfam domains (4) ----Methuselah_N-2pzxD04 D:5-185                                                                                                                                                         --- Pfam domains (4)
         Sec.struct. author .....hhhhhee....ee.....eee..eeehhh.eeeeeeee.....eeeeeeeeee.hhhh..eee.......eee..eee...hhhhhh.ee.eeeee.....eeeee.....eee..........ee....hhhh.eeee....eee....eee....eeeeeee........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------I-----------------------------------------------------------------------------A------------------N------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzx D   1 DILECDYFDTVDISAAQKLQNGSYLFEGLLVPAILTGEYDFRILPDDSKQKVARHIRGCVCKLKPCVRFCCPHDHIMDNGVCYDNMSDEELAELDPFLNVTLDDGSVSRRHFKNELIVQWDLPMPCDGMFYLDNREEQDKYTLFENGTFFRHFDRVTLRKREYCLQHLTFADGNATSIRIAPHNCLIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        

   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  (2, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MTH_DROME | O97148)
molecular function
    GO:0008528    G-protein coupled peptide receptor activity    Combining with a peptide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0006836    neurotransmitter transport    The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:1901562    response to paraquat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paraquat stimulus.
    GO:0000302    response to reactive oxygen species    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    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:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0098793    presynapse    The part of a synapse that is part of the presynaptic cell.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTH_DROME | O971481fjr

(-) Related Entries Specified in the PDB File

1fjr