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(-) Description

Title :  SOLUTION STRUCTURE OF PDZ DOMAIN OF PDZ AND LIM DOMAIN PROTEIN
 
Authors :  T. N. Niraula, T. Tomizawa, K. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Feb 07  (Deposition) - 21 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Pdz And Lim Domain, 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, T. Tomizawa, K. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of Pdz Domain Of Pdz And Lim Domain Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PDZ AND LIM DOMAIN PROTEIN 4
    Chains: A
    Engineered: YES
    Expression System Plasmid: P050627-04
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Gene: PDLIM4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: LIM PROTEIN RIL, REVERSION-INDUCED LIM PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 2EEG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:16 -Pro A:17
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PDLI4_HUMAN8-84  1A:15-88

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002537541aENSE00001042731chr5:131593364-131593520157PDLI4_HUMAN1-31311A:8-3831
1.3ENST000002537543ENSE00001713905chr5:131598302-131598453152PDLI4_HUMAN32-82511A:39-8850
1.4aENST000002537544aENSE00000899290chr5:131602157-13160223882PDLI4_HUMAN82-109280--
1.6aENST000002537546aENSE00000899292chr5:131606608-131606786179PDLI4_HUMAN110-169601A:89-946
1.6eENST000002537546eENSE00000899294chr5:131606996-131607159164PDLI4_HUMAN169-224560--
1.6hENST000002537546hENSE00000899296chr5:131607484-131607601118PDLI4_HUMAN224-263400--
1.7cENST000002537547cENSE00001909392chr5:131607718-1316091471430PDLI4_HUMAN263-330680--

(-) 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:94
 aligned with PDLI4_HUMAN | P50479 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:136
                                   1                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123      
          PDLI4_HUMAN     - -------MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEIQDGSPTTSRRPSGTGTGPEDG 129
               SCOP domains d2eega_ A: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.........ee.........ee......hhhhhh......eeeee..ee....hhhhhhhhhhh....eeeeee------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PDZ  PDB: A:15-88 UniProt: 8-84                                              --------------------------------------------- PROSITE
           Transcript 1 (1) -------Exon 1.1a  PDB: A:8-38         Exon 1.3  PDB: A:39-88 UniProt: 32-82 [INCOMPLETE] ---------------------------Exon 1.6a            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.4a  PDB: -           -------------------- Transcript 1 (2)
                 2eeg A   1 GSSGSSGMPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVS------------------------------------------SGPSSG  94
                                    10        20        30        40        50        60        70        80       | -         -         -         -         -|     
                                                                                                                  88                                         89
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (PDLI4_HUMAN | P50479)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.

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 Related Entries

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        PDLI4_HUMAN | P50479: 2v1w 4q2o

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