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 :  IODIDE DERIVATIVE OF HUMAN LFABP
 
Authors :  A. Sharma, M. Yogavel, A. Sharma
Date :  03 Aug 11  (Deposition) - 20 Jun 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Lfabp, Iodide, Copper Kalpha, Palmitic Acid, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Sharma, M. Yogavel, A. Sharma
Utility Of Anion And Cation Combinations For Phasing Of Protein Structures.
J. Struct. Funct. Genom. V. 13 135 2012
PubMed-ID: 22562242  |  Reference-DOI: 10.1007/S10969-012-9137-3

(-) Compounds

Molecule 1 - FATTY ACID-BINDING PROTEIN, LIVER
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainB834
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFABP1, FABPL
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFATTY ACID-BINDING PROTEIN 1, LIVER-TYPE FATTY ACID-BINDING PROTEIN, L-FABP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1IOD5Ligand/IonIODIDE ION
2PLM2Ligand/IonPALMITIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:39 , PHE A:63 , PHE A:95 , THR A:102 , ILE A:109 , ASN A:111 , MET A:113 , ARG A:122 , HOH A:141 , PLM A:151BINDING SITE FOR RESIDUE PLM A 150
2AC2SOFTWAREPHE A:15 , LEU A:28 , ILE A:52 , ALA A:54 , GLY A:55 , MET A:74 , ASN A:111 , ARG A:122 , PLM A:150BINDING SITE FOR RESIDUE PLM A 151
3AC3SOFTWAREMET A:74BINDING SITE FOR RESIDUE IOD A 130
4AC4SOFTWAREGLN A:12 , LYS A:36BINDING SITE FOR RESIDUE IOD A 131
5AC5SOFTWAREGLU A:40 , LYS A:49 , PHE A:50 , THR A:51BINDING SITE FOR RESIDUE IOD A 132
6AC6SOFTWAREGLU A:13BINDING SITE FOR RESIDUE IOD A 133

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VG2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VG2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014662A54TFABPL_HUMANPolymorphism1801273AA54T
2UniProtVAR_022093T94AFABPL_HUMANPolymorphism2241883AT94A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.FABPL_HUMAN5-22  1A:5-22

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002958341aENSE00001876850chr2:88427635-88427470166FABPL_HUMAN1-23231A:1-2323
1.3aENST000002958343aENSE00001076276chr2:88425867-88425695173FABPL_HUMAN23-80581A:23-8058
1.4aENST000002958344aENSE00001076280chr2:88424105-8842401393FABPL_HUMAN81-111311A:81-11131
1.4dENST000002958344dENSE00001076278chr2:88422623-88422510114FABPL_HUMAN112-127161A:112-12716

(-) 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:129
 aligned with FABPL_HUMAN | P07148 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:129
                                                                                                                                                        127  
                                    10        20        30        40        50        60        70        80        90       100       110       120      |  
          FABPL_HUMAN     1 MSFSGKYQLQSQENFEAFMKAIGLPEELIQKGKDIKGVSEIVQNGKHFKFTITAGSKVIQNEFTVGEECELETMTGEKVKTVVQLEGDNKLVTTFKNIKSVTELNGDIITNTMTLGDIVFKRISKRI--   -
               SCOP domains d3vg2a_ A: Liver fatty acid binding protein                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhhh.hhhhhhhhh....eeeeeee..eeeeeeee..eeeeeeee...eeeee.....eeeeeeeee...eeeeee..eeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------T---------------------------------------A----------------------------------- SAPs(SNPs)
                    PROSITE ----FABP  PDB: A:5-22 ----------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-23 ---------------------------------------------------------Exon 1.4a  PDB: A:81-111       Exon 1.4d       -- Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.3a  PDB: A:23-80 UniProt: 23-80                    ------------------------------------------------- Transcript 1 (2)
                 3vg2 A   1 SSFSGKYQLQSQENFEAFMKAIGLPEELIQKGKDIKGVSEIVQNGKHFKFTITAGSKVIQNEFTVGEECELETMTGEKVKTVVQLEGDNKLVTTFKNIKSVTELNGDIITNTMTLGDIVFKRISKRIGT 129
                                    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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VG2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VG2)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FABPL_HUMAN | P07148)
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: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:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    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: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:0019433    triglyceride catabolic process    The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
    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.

 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
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLM  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vg2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3vg2
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FABPL_HUMAN | P07148
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FABPL_HUMAN | P07148
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FABPL_HUMAN | P071482f73 2l67 2l68 2lkk 2py1 3b2h 3b2i 3b2j 3b2k 3b2l 3stk 3stm 3stn 3vg3 3vg4 3vg5 3vg6 3vg7

(-) Related Entries Specified in the PDB File

3b2h 3b2i 3b2j 3b2k 3b2l 3vg3 3vg4 3vg5 3vg6 3vg7