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(-) Description

Title :  THE 5TH PDZ DOMAIN OF INAD IN 10MM DTT
 
Authors :  R. Ranganathan, M. Socolich, M. Wall
Date :  11 Jul 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,C  (2x)
Keywords :  Pdz Domain; Scaffolding Protein; Disulfide Bond, Membrane, Sensory Transduction, Vision, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Mishra, M. Socolich, M. A. Wall, J. Graves, Z. Wang, R. Ranganathan
Dynamic Scaffolding In A G Protein-Coupled Signaling System
Cell(Cambridge, Mass. ) V. 131 80 2007
PubMed-ID: 17923089  |  Reference-DOI: 10.1016/J.CELL.2007.07.037

(-) Compounds

Molecule 1 - INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-5X-3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Fragment5TH PDZ DOMAIN
    GeneINAD
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (2x) BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:594 , LEU B:595 , GLY B:596 , LEU B:597 , PHE B:649 , HOH B:675BINDING SITE FOR RESIDUE GOL B 1
2AC2SOFTWAREHOH C:75 , HOH C:114 , HOH C:169 , GLU C:594 , LEU C:595 , GLY C:596 , LEU C:597 , PHE C:649BINDING SITE FOR RESIDUE GOL C 2

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:606 -C:645

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QKU)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.INAD_DROME17-106
249-332
364-448
584-664
 
 
489-552
  3-
-
-
A:584-664
B:584-663
C:584-664
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.INAD_DROME17-106
249-332
364-448
584-664
 
 
489-552
  1-
-
-
A:584-664
-
-
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.INAD_DROME17-106
249-332
364-448
584-664
 
 
489-552
  4-
-
-
-
B:584-663
C:584-664
-

(-) Exons   (0, 0)

(no "Exon" information available for 2QKU)

(-) 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:85
 aligned with INAD_DROME | Q24008 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:85
                                   589       599       609       619       629       639       649       659     
           INAD_DROME   580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPK 664
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeee..eeeeeee....hhhhhhhh....eeeee..ee....hhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:584-664 UniProt: 584-664                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2qku A 580 LEKFNVDLmKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSmEVTRPK 664
                                   589       599       609       619       629       639       649       659     
                                  588-MSE                                                               658-MSE  

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with INAD_DROME | Q24008 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:84
                                   589       599       609       619       629       639       649       659    
           INAD_DROME   580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRP 663
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee........eeeeee..eeeeeee....hhhhhhhh....eeeee..ee....hhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:584-663 UniProt: 584-664                                             PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2qku B 580 LEKFNVDLmKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSmEVTRP 663
                                   589       599       609       619       629       639       649       659    
                                  588-MSE                                                               658-MSE 

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with INAD_DROME | Q24008 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:90
                                   589       599       609       619       629       639       649       659       669
           INAD_DROME   580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPKPTLRT 669
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----PDZ-2qkuC01 C:584-661                                                         -------- Pfam domains (1)
           Pfam domains (2) ----PDZ-2qkuC02 C:584-661                                                         -------- Pfam domains (2)
           Pfam domains (3) ----PDZ-2qkuC03 C:584-661                                                         -------- Pfam domains (3)
         Sec.struct. author .eeeeeeeee.......eeeeee..eeeeeee....hhhhhhhh....eeeee..ee....hhhhhhh......eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PDZ  PDB: C:584-664 UniProt: 584-664                                             ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2qku C 580 LEKFNVDLmKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSmEVTRPKPAAAS 669
                                   589       599       609       619       629       639       649       659       669
                                  588-MSE                                                               658-MSE       

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

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2QKU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QKU)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (INAD_DROME | Q24008)
molecular function
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0031473    myosin III binding    Interacting selectively and non-covalently with a class III myosin; myosin III is monomeric and has an N terminal kinase domain.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
    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:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0071482    cellular response to light stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0016059    deactivation of rhodopsin mediated signaling    The process of restoring the photoreceptor cell to its unexcited state after termination of the stimulus (photon).
    GO:0050962    detection of light stimulus involved in sensory perception    The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light.
    GO:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0050896    response to stimulus    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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0016027    inaD signaling complex    A complex of proteins that are involved in phototransduction and attached to the transient receptor potential (TRP) channel. The protein connections are mediated through inaD.
    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:0016028    rhabdomere    The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        INAD_DROME | Q240081ihj 2la8 2qkt 2qkv 3r0h 5f67

(-) Related Entries Specified in the PDB File

2qkt 2qkv