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(-) Description

Title :  SOLUTION-STATE STRUCTURES OF OLEATE-LIGANDED LFABP, MAJOR FORM OF 1:2 PROTEIN-LIGAND COMPLEX
 
Authors :  Y. He, X. Yang, H. Wang, R. Estephan, F. Francis, S. Kodukula, J. Storch, R. E. Stark
Date :  15 Aug 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Protein, Apo, Lfabp, Ilbp, Fabp, Acetylation, Cytoplasm, Lipid-Binding, Phosphorylation, Transport, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. He, X. Yang, H. Wang, R. Estephan, F. Francis, S. Kodukula, J. Storch, R. E. Stark
Solution-State Molecular Structure Of Apo And Oleate-Liganded Liver Fatty Acid-Binding Protein
Biochemistry V. 46 12543 2007
PubMed-ID: 17927211  |  Reference-DOI: 10.1021/BI701092R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FATTY ACID-BINDING PROTEIN, LIVER
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VariantPLYS
    Expression System VectorPET-11A
    Expression System Vector TypeVECTOR
    GeneFABP1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymL-FABP, Z-PROTEIN, SQUALENE- AND STEROL-CARRIER PROTEIN, SCP, P14

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1OLA2Ligand/IonOLEIC ACID

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:54 , ASN A:61BINDING SITE FOR RESIDUE OLA A 128
2AC2SOFTWAREILE A:41 , PHE A:63 , LEU A:71 , VAL A:83 , THR A:102 , ILE A:109 , ARG A:122BINDING SITE FOR RESIDUE OLA A 129

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JU8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JU8)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.FABPL_RAT5-22  1A:5-22

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000088401ENSRNOE00000061099chr4:104412205-104412306102FABPL_RAT1-23231A:1-2323
1.2ENSRNOT000000088402ENSRNOE00000061517chr4:104413761-104413933173FABPL_RAT23-80581A:23-8058
1.3ENSRNOT000000088403ENSRNOE00000061670chr4:104415158-10441525093FABPL_RAT81-111311A:81-11131
1.4ENSRNOT000000088404ENSRNOE00000061878chr4:104415861-104415981121FABPL_RAT112-127161A:112-12716

(-) 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:127
 aligned with FABPL_RAT | P02692 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
            FABPL_RAT     1 MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKSVTEFNGDTITNTMTLGDIVYKRVSKRI 127
               SCOP domains d2ju8a_ A: Liver fatty acid binding protein                                                                                     SCOP domains
               CATH domains 2ju8A00 A:1-127  [code=2.40.128.20, no name defined]                                                                            CATH domains
               Pfam domains ---Lipocalin-2ju8A01 A:4-127                                                                                                    Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhh.hhhhhhhhhh...eeeeeee..eeeeeeee..eeeeeeee..eeeeee.....eeeeeeee.....eeeee..eeeeeee...eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----FABP  PDB: A:5-22 --------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-23  ---------------------------------------------------------Exon 1.3  PDB: A:81-111        Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.2  PDB: A:23-80 UniProt: 23-80                     ----------------------------------------------- Transcript 1 (2)
                 2ju8 A   1 MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKSVTEFNGDTITNTMTLGDIVYKRVSKRI 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Calycin (163)

(-) Gene Ontology  (34, 34)

NMR Structure(hide GO term definitions)
Chain A   (FABPL_RAT | P02692)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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:0005324    long-chain fatty acid transporter activity    Enables the directed movement of long-chain fatty acids into, out of or within a cell, or between cells. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    GO:0051978    lysophospholipid transporter activity    Enables the directed movement of lysophospholipids into, out of or within a cell, or between cells. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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: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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0070301    cellular response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0050892    intestinal absorption    Any process in which nutrients are taken up from the contents of the intestine.
    GO:0015909    long-chain fatty acid transport    The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    GO:0051977    lysophospholipid transport    The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids.
    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:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0032000    positive regulation of fatty acid beta-oxidation    Any process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation.
    GO:0051345    positive regulation of hydrolase activity    Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    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:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    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: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.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    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
        FABPL_RAT | P026921lfo 2ju3 2ju7

(-) Related Entries Specified in the PDB File

4098 RESONANCE ASSIGNMENTS AND SECONDARY STRUCTURE RELATED ID: 15429 RELATED DB: BMRB SOLUTION-STATE STRUCTURES OF APO-LFABP (LIVER FATTY ACID- BINDING PROTEIN)
2ju3 SOLUTION-STATE STRUCTURES OF APO-LFABP (LIVER FATTY ACID- BINDING PROTEIN) RELATED ID: 15433 RELATED DB: BMRB SOLUTION-STATE STRUCTURES OF OLEATE-LIGANDED LFABP, PROTEIN ONLY
2ju7 SOLUTION-STATE STRUCTURES OF OLEATE-LIGANDED LFABP, PROTEIN ONLY RELATED ID: 15434 RELATED DB: BMRB