Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF FIRST LIM DOMAIN OF ENIGMA-LIKE PDZ AND LIM DOMAINS PROTEIN
 
Authors :  T. N. Niraula, Y. Muto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Dec 05  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lim Domain, Enigma Homolog Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. N. Niraula, Y. Muto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of First Lim Domain Of Enigma-Like Pdz And Lim Domains Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PDZ AND LIM DOMAIN PROTEIN 5
    ChainsA
    EngineeredYES
    Expression System PlasmidP050302-83
    Expression System Vector TypePLASMID
    FragmentLIM DOMAIN
    GeneENH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymENIGMA HOMOLOG, ENIGMA-LIKE PDZ AND LIM DOMAINS PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , CYS A:31 , HIS A:48 , GLU A:51BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:54 , CYS A:57 , CYS A:75 , CYS A:78BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DAR)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.PDLI5_HUMAN477-536
418-476
537-596
  2A:86-90
A:26-84
-
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.PDLI5_HUMAN479-512
538-573
  1A:86-90
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003179681cENSE00001912006chr4:95373053-9537314694PDLI5_HUMAN-00--
1.2bENST000003179682bENSE00002170638chr4:95376398-95376535138PDLI5_HUMAN1-32320--
1.6aENST000003179686aENSE00001175751chr4:95444875-95445026152PDLI5_HUMAN33-83510--
1.8aENST000003179688aENSE00001238156chr4:95494502-9549454443PDLI5_HUMAN83-97150--
1.9bENST000003179689bENSE00001071717chr4:95496767-95497185419PDLI5_HUMAN98-2371400--
1.15aENST0000031796815aENSE00001003998chr4:95506716-95506888173PDLI5_HUMAN237-295590--
1.16ENST0000031796816ENSE00001003997chr4:95507559-9550759537PDLI5_HUMAN295-307130--
1.21bENST0000031796821bENSE00001003996chr4:95539155-95539342188PDLI5_HUMAN307-370641A:1-44
1.22ENST0000031796822ENSE00001137857chr4:95561427-95561601175PDLI5_HUMAN370-428591A:5-36 (gaps)57
1.23ENST0000031796823ENSE00001137849chr4:95575611-95575791181PDLI5_HUMAN428-488611A:36-90 (gaps)61
1.25ENST0000031796825ENSE00001137840chr4:95578578-95578698121PDLI5_HUMAN489-529410--
1.26ENST0000031796826ENSE00001137833chr4:95583573-95583688116PDLI5_HUMAN529-567390--
1.27dENST0000031796827dENSE00001948294chr4:95585129-955893744246PDLI5_HUMAN568-596290--

(-) Sequences/Alignments

NMR Structure
   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:90
 aligned with PDLI5_HUMAN | Q96HC4 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:136
                                   362       372       382       392       402       412       422       432       442       452       462       472       482      
          PDLI5_HUMAN   353 GSTGVIKSPSWQRPNQGVPSTGRISNSATYSGSVAPANSALGQTQPSDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFAPECGRCQRKILG 488
               SCOP domains -----------------------------------------------d2dara2 A:8-52                               d2dara1 A:53-84                 ------------ SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------...-------------------------.........eee...................eeee..eee...................ee....eehhhhhhhhh.--.....----. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------LIM_DOMAIN_2  PDB: A:26-84 UniProt: 418-476                LIM_DOMAIN_2 PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------LIM_DOMAIN PROSITE (2)
           Transcript 1 (1) Exon 1.21b        ---------------------------------------------------------Exon 1.23  PDB: A:36-90 (gaps) UniProt: 428-488               Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.22  PDB: A:5-36 (gaps) UniProt: 370-428 [INCOMPLETE]------------------------------------------------------------ Transcript 1 (2)
                 2dar A   1 GSSG---------------SSG-------------------------DQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFA--SGPSS----G  90
                               |     -         5 |       -         -       |10        20        30        40        50        60        70        80   |  | 88|    |
                               4               5 7                         8                                                                          84 85  89   90

   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, 2)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DAR)

(-) Gene Ontology  (21, 24)

NMR Structure(hide GO term definitions)
Chain A   (PDLI5_HUMAN | Q96HC4)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0042805    actinin binding    Interacting selectively and non-covalently with actinin, any member of a family of proteins that crosslink F-actin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0061049    cell growth involved in cardiac muscle cell development    The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
    GO:0061001    regulation of dendritic spine morphogenesis    Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0051963    regulation of synapse assembly    Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    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: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.

 Visualization

(-) Interactive Views

NMR Structure
  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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dar)
 

(-) 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
  2dar
    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
  PDLI5_HUMAN | Q96HC4
    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
  PDLI5_HUMAN | Q96HC4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDLI5_HUMAN | Q96HC42uzc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DAR)