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(-) Description

Title :  TROGLITAZONE BOUND TO FATTY ACID BINDING PROTEIN 4
 
Authors :  R. E. Gillilan, S. D. Ayers, N. Noy
Date :  14 Jul 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Clamshell, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. E. Gillilan, S. D. Ayers, N. Noy
Structural Basis For Activation Of Fatty Acid-Binding Protein 4
J. Mol. Biol. V. 372 1246 2007
PubMed-ID: 17761196  |  Reference-DOI: 10.1016/J.JMB.2007.07.040

(-) Compounds

Molecule 1 - FATTY ACID-BINDING PROTEIN, ADIPOCYTE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneFABP4, AP2
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAFABP, ADIPOCYTE LIPID-BINDING PROTEIN, ALBP, A-FABP, P2 ADIPOCYTE PROTEIN, MYELIN P2 PROTEIN HOMOLOG, 3T3-L1 LIPID-BINDING PROTEIN, 422 PROTEIN, P15

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2TDZ2Ligand/Ion(5R)-5-(4-{[(2R)-6-HYDROXY-2,5,7,8-TETRAMETHYL-3,4-DIHYDRO-2H-CHROMEN-2-YL]METHOXY}BENZYL)-1,3-THIAZOLIDINE-2,4-DIONE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:13 , GLU B:14 , ASN B:15 , PHE B:16 , ASP B:17BINDING SITE FOR RESIDUE SO4 B 302
2AC2SOFTWARESER A:13 , GLU A:14 , ASN A:15 , PHE A:16 , ASP A:17 , HOH A:337BINDING SITE FOR RESIDUE SO4 A 303
3AC3SOFTWARESER A:-5 , ARG A:108 , ARG A:130 , ARG B:108 , ARG B:130BINDING SITE FOR RESIDUE SO4 A 301
4AC4SOFTWARETYR A:19 , VAL A:25 , PHE A:57 , ASP A:76 , ARG A:78 , CYS A:117 , TYR A:128 , HOH A:339BINDING SITE FOR RESIDUE TDZ A 201
5AC5SOFTWARETYR B:19 , MET B:20 , VAL B:25 , ASP B:76 , ARG B:78 , ILE B:104 , CYS B:117BINDING SITE FOR RESIDUE TDZ B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QM9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:-7 -Ser A:-6
2Ser A:-5 -Lys A:-4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QM9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.FABP4_MOUSE7-24
 
  2A:6-23
B:6-23

(-) Exons   (0, 0)

(no "Exon" information available for 2QM9)

(-) 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:139
 aligned with FABP4_MOUSE | P04117 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:139
                                   1                                                                                                                                   
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123         
          FABP4_MOUSE     - -------MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 132
               SCOP domains d2qm9a_ A: Adipocyte lipid-binding protein, ALBP                                                                                            SCOP domains
               CATH domains 2qm9A00 A:-7-131  [code=2.40.128.20, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeehhhhhhhhhh.hhhhhhhhhh...eeeeeee..eeeeeee.....eeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------FABP  PDB: A:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm9 A  -7 SSSKVYKMCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 131
                                     2        12        22        32        42        52        62        72        82        92       102       112       122         

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with FABP4_MOUSE | P04117 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
          FABP4_MOUSE     1 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 132
               SCOP domains d2qm9b_ B: Adipocyte lipid-binding protein, ALBP                                                                                     SCOP domains
               CATH domains 2qm9B00 B:0-131  [code=2.40.128.20, no name defined]                                                                                 CATH domains
           Pfam domains (1) -----Lipocalin-2qm9B01 B:5-131                                                                                                       Pfam domains (1)
           Pfam domains (2) -----Lipocalin-2qm9B02 B:5-131                                                                                                       Pfam domains (2)
         Sec.struct. author hhhhh.eeeeeeeeehhhhhhhhhh.hhhhhhhhhh...eeeeeee..eeeeeee.....eeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------FABP  PDB: B:6-23 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qm9 B   0 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129  

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FABP4_MOUSE | P04117)
molecular function
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0071285    cellular response to lithium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0050872    white fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FABP4_MOUSE | P041171a18 1a2d 1ab0 1acd 1adl 1alb 1g74 1g7n 1lib 1lic 1lid 1lie 1lif 2ans 2q9s 3hk1 3js1 3jsq 5c0n 5d8j

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QM9)