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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FK506-BINDING DOMAIN OF HUMAN FKBP38
 
Authors :  C. Parthier, M. Maestre-Martinez, P. Neumann, F. Edlich, G. Fischer, C M. T. Stubbs
Date :  19 Oct 08  (Deposition) - 27 Oct 09  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Half-Barrel, Ppiase, Immunophilin, Apoptosis, Host-Virus Interaction, Isomerase, Membrane, Mitochondrion, Phosphoprotein, Rotamase, Tpr Repeat, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Maestre-Martinez, K. Haupt, F. Edlich, P. Neumann, C. Parthier, M. T. Stubbs, G. Fischer, C. Luecke
A Charge-Sensitive Loop In The Fkbp38 Catalytic Domain Modulates Bcl-2 Binding.
J. Mol. Recognit. V. 24 23 2011
PubMed-ID: 20140889  |  Reference-DOI: 10.1002/JMR.1020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FK506-BINDING PROTEIN 8
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFK506 BINDING DOMAIN
    GeneFKBP38, FKBP8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 38 KDA FK506-BINDING PROTEIN, HFKBP38, FKBPR38

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3EY6)

(-) Sites  (0, 0)

(no "Site" information available for 3EY6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EY6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:128 -Pro A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EY6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP8_HUMAN120-204  1A:63-147

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002223081ENSE00001419038chr19:18654383-1865429688FKBP8_HUMAN-00--
1.2ENST000002223082ENSE00001123589chr19:18652805-18652489317FKBP8_HUMAN1-98981A:33-41 (gaps)19
1.3ENST000002223083ENSE00000691184chr19:18650530-18650361170FKBP8_HUMAN98-154571A:41-9757
1.4ENST000002223084ENSE00000691186chr19:18650269-1865018189FKBP8_HUMAN155-184301A:98-12730
1.5aENST000002223085aENSE00000866219chr19:18649246-18649026221FKBP8_HUMAN184-258751A:127-15024
1.6ENST000002223086ENSE00000691191chr19:18648583-18648411173FKBP8_HUMAN258-315580--
1.7ENST000002223087ENSE00000691193chr19:18644157-1864408078FKBP8_HUMAN316-341260--
1.8ENST000002223088ENSE00000691195chr19:18643605-18643474132FKBP8_HUMAN342-385440--
1.9bENST000002223089bENSE00000866220chr19:18643065-18642568498FKBP8_HUMAN386-413280--

(-) 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:118
 aligned with FKBP8_HUMAN | Q14318 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:128
                                    89        99       109       119       129       139       149       159       169       179       189       199        
          FKBP8_HUMAN    80 MEPEPAPAPAPEEWLDILGNGLLRKKTLVPGPPGSSRPVKGQVVTVHLQTSLENGTRVQEEPELVFTLGDCDVIQALDLSVPLMDVGETAMVTADSKYCYGPQGRSPYIPPHAALCLEVTLKTAVDGP 207
               SCOP domains d3          ey6a_ A: automated matches                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------..ee......eeeeeee.............eeeeeeeeee....eeeeeeeeeee.......hhhhhhhhhh....eeeeee.hhh..hhh...........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------FKBP_PPIASE  PDB: A:63-147 UniProt: 120-204                                          --- PROSITE
           Transcript 1 (1) Exon 1.2           --------------------------------------------------------Exon 1.4  PDB: A:98-127       ----------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3  PDB: A:41-97 UniProt: 98-154                   -----------------------------Exon 1.5a  PDB: A:127-15 Transcript 1 (2)
                 3ey6 A  33 MR----------EWLDILGNGLLRKKTLVPGPPGSSRPVKGQVVTVHLQTSLENGTRVQEEPELVFTLGDCDVIQALDLSVPLMDVGETAMVTADSKYCYGPQGRSPYIPPHAALCLEVTLKTAVDGP 150
                             |       -  |     42        52        62        72        82        92       102       112       122       132       142        
                             |         35                                                                                                                   
                            34                                                                                                                              

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EY6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EY6)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FKBP8_HUMAN | Q14318)
molecular function
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0001708    cell fate specification    The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
    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:0021904    dorsal/ventral neural tube patterning    The process in which the neural tube is regionalized in the dorsoventral axis.
    GO:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0021915    neural tube development    The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0030510    regulation of BMP signaling pathway    Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum 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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FKBP8_HUMAN | Q143182awg 2d9f 2f2d 2mf9 5mgx

(-) Related Entries Specified in the PDB File

6902 CHEMICAL SHIFT ASSIGNMENTS
2awg CRYSTAL STRUCTURE AT 1.6 A
2f2d NMR STRUCTURE