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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PEX19P
 
Authors :  N. Schueller, S. J. Holton, W. A. Stanley, Y. H. Song, P. Konarev, M. Roes R. Erdmann, W. Schliebs, M. Wilmanns
Date :  22 Jun 09  (Deposition) - 23 Jun 10  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
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 :  Protein Transport, Biogenesis Disorder, Zellweger Syndrome, Membrane, Prenylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Schueller, S. J. Holton, K. Fodor, M. Milewski, P. Konarev, W. A. Stanley, J. Wolf, R. Erdmann, W. Schliebs, Y. H. Song, M. Wilmanns
The Peroxisomal Receptor Pex19P Forms A Helical Mpts Recognition Domain.
Embo J. V. 29 2491 2010
PubMed-ID: 20531392  |  Reference-DOI: 10.1038/EMBOJ.2010.115

(-) Compounds

Molecule 1 - PEROXISOMAL BIOGENESIS FACTOR 19
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPETM-11
    FragmentRESIDUES 161-283
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEROXIN-19, PEROXISOMAL FARNESYLATED PROTEIN, 33 KDA HOUSEKEEPING PROTEIN

 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 2WL8)

(-) Sites  (0, 0)

(no "Site" information available for 2WL8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WL8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WL8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WL8)

(-) Exons   (0, 0)

(no "Exon" information available for 2WL8)

(-) 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:110
 aligned with PEX19_HUMAN | P40855 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:110
                                   180       190       200       210       220       230       240       250       260       270       280
          PEX19_HUMAN   171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDL 280
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2wl8 A 171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFDL 280
                                   180       190       200       210       220       230       240       250       260       270       280

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with PEX19_HUMAN | P40855 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:104
                                   180       190       200       210       220       230       240       250       260       270    
          PEX19_HUMAN   171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPP 274
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2wl8 B 171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPP 274
                                   180       190       200       210       220       230       240       250       260       270    

Chain C from PDB  Type:PROTEIN  Length:109
 aligned with PEX19_HUMAN | P40855 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:109
                                   180       190       200       210       220       230       240       250       260       270         
          PEX19_HUMAN   171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFD 279
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wl8 C 171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFD 279
                                   180       190       200       210       220       230       240       250       260       270         

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with PEX19_HUMAN | P40855 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:109
                                   180       190       200       210       220       230       240       250       260       270         
          PEX19_HUMAN   171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFD 279
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Pex19-2wl8D01 D:171-279                                                                                       Pfam domains (1)
           Pfam domains (2) Pex19-2wl8D02 D:171-279                                                                                       Pfam domains (2)
           Pfam domains (3) Pex19-2wl8D03 D:171-279                                                                                       Pfam domains (3)
           Pfam domains (4) Pex19-2wl8D04 D:171-279                                                                                       Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wl8 D 171 ILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQDLGHPPKELAGEMPPGLNFD 279
                                   180       190       200       210       220       230       240       250       260       270         

   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 2WL8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WL8)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
1aPex19-2wl8D01D:171-279
1bPex19-2wl8D02D:171-279
1cPex19-2wl8D03D:171-279
1dPex19-2wl8D04D:171-279

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PEX19_HUMAN | P40855)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0036105    peroxisome membrane class-1 targeting sequence binding    Interacting selectively and non-covalently with a class I peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-dependent manner.
    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).
biological process
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0072321    chaperone-mediated protein transport    The directed movement of proteins into, out of or within a cell, or between cells, mediated by chaperone molecules that bind to the transported proteins.
    GO:0072663    establishment of protein localization to peroxisome    The directed movement of a protein to a specific location in a peroxisome.
    GO:1900131    negative regulation of lipid binding    Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding.
    GO:0016559    peroxisome fission    The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments.
    GO:0016557    peroxisome membrane biogenesis    The process in which a peroxisome membrane is synthesized, aggregates, and bonds together.
    GO:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0045046    protein import into peroxisome membrane    The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0006625    protein targeting to peroxisome    The process of directing proteins towards the peroxisome, usually using signals contained within the protein.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PEX19_HUMAN | P408552w85 3ajb 3mk4 5lnf

(-) Related Entries Specified in the PDB File

2w85 STRUCTURE OF PEX14 IN COMPEX WITH PEX19