Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PARVULIN 14
 
Authors :  J. W. Mueller, N. M. Link, A. Matena, L. Hoppstock, A. Rueppel, P. Bayer, W. Blankenfeldt
Date :  04 Nov 11  (Deposition) - 07 Dec 11  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidyl-Prolyl-Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Mueller, N. M. Link, A. Matena, L. Hoppstock, A. Ruppel, P. Bayer, W. Blankenfeldt
Crystallographic Proof For An Extended Hydrogen-Bonding Network In Small Prolyl Isomerases.
J. Am. Chem. Soc. V. 133 20096 2011
PubMed-ID: 22081960  |  Reference-DOI: 10.1021/JA2086195

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 4
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-41
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PIN4, Q9Y237
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARVULIN-14, PAR14, HPAR14, PARVULIN-17, PAR17, HPAR17, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PIN4, PPIASE PIN4, PEPTIDYL- PROLYL CIS/TRANS ISOMERASE EPVH, HEPVH, ROTAMASE PIN4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1D1D1Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
2NA2Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:74 , LYS A:75 , ALA A:76 , ARG A:77 , HOH A:322 , HOH A:332 , HOH A:370 , HOH A:400 , HOH A:426 , HOH A:457BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREGLY A:83 , TRP A:84 , VAL A:91 , GLY A:92 , HOH A:357 , HOH A:383 , HOH A:386 , HOH A:409 , HOH A:451BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREARG A:87 , GLN A:95 , HOH A:350 , HOH A:369 , HOH A:401 , HOH A:424BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREGLY A:105 , MET A:106 , ASP A:107 , LYS A:108 , LYS A:117 , HOH A:314 , HOH A:343 , HOH A:353 , HOH A:360 , HOH A:405BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWAREHIS A:42 , ASP A:74 , TRP A:84 , PHE A:120 , HIS A:123 , LYS A:131BINDING SITE FOR RESIDUE D1D A 205
6AC6SOFTWAREHIS A:48 , LYS A:59 , ASP A:107 , HOH A:449BINDING SITE FOR RESIDUE NA A 206
7AC7SOFTWAREVAL A:91 , PRO A:93 , THR A:118 , LYS A:119 , HOH A:341 , HOH A:409BINDING SITE FOR RESIDUE NA A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UI5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UI5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPIC_PPIASE_2PS50198 PpiC-type peptidyl-prolyl cis-trans isomerase family profile.PIN4_HUMAN35-129  1A:36-129

(-) Exons   (0, 0)

(no "Exon" information available for 3UI5)

(-) Sequences/Alignments

Asymmetric/Biological 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:101
 aligned with PIN4_HUMAN | Q9Y237 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:102
                                    39        49        59        69        79        89        99       109       119       129  
           PIN4_HUMAN    30 GPKGGGNAVKVRHILCEKHGKIMEAMEKLKSGMRFNEVAAQYSEDKARQGGDLGWMTRGSMVGPFQEAAFALPVSGMDKPVFTDPPVKTKFGYHIIMVEGRK 131
               SCOP domains d3ui 5a_ A: automated matches                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhh-h.eeeeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhh..hhhhh.eeeeee....hhhhhhhhhh...............eee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----PPIC_PPIASE_2  PDB: A:36-129 UniProt: 35-129                                                   -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3ui5 A  -4 GPMG-SNAVKVRHILCEKHGKIMEAMEKLKSGMRFNEVAAQYSEDKARQGGDLGWMTRGSMVGPFQEAAFALPVSGMDKPVFTDPPVKTKFGYHIIMVEGRK 131
                               | || 39        49        59        69        79        89        99       109       119       129  
                              -1 0|                                                                                               
                                 36
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UI5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UI5)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIN4_HUMAN | Q9Y237)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003681    bent DNA binding    Interacting selectively and non-covalently with DNA in a bent conformation.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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).
biological process
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0030684    preribosome    Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    D1D  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:113 - Pro A:114   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ui5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PIN4_HUMAN | Q9Y237
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.2.1.8
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PIN4_HUMAN | Q9Y237
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PIN4_HUMAN | Q9Y237: 1eq3 1fjd 3ui4 3ui6

(-) Related Entries Specified in the PDB File

3ui4 3ui6