Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYALINE DROPLET INDUCER.
 
Authors :  B. N. Chaudhuri, G. J. Kleywegt, T. A. Jones
Date :  19 Nov 98  (Deposition) - 13 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lipid-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. N. Chaudhuri, G. J. Kleywegt, J. Bjorkman, L. D. Lehman-Mckeeman, J. D. Oliver, T. A. Jones
The Structures Of Alpha 2U-Globulin And Its Complex With A Hyaline Droplet Inducer.
Acta Crystallogr. , Sect. D V. 55 753 1999
PubMed-ID: 10089305  |  Reference-DOI: 10.1107/S0907444998017211
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ALPHA-2U-GLOBULIN)
    ChainsA, B, C, D
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsD-LIMONENE 1,2-EPOXIDE (NOT INCLUDED IN THE REFINEMENT)
    Other Details - SourcePURIFIED FROM MALE RAT URINE
    SecretionURINE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1LEO4Ligand/IonD-LIMONENE 1,2-EPOXIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:38 , PHE A:54 , TYR A:120BINDING SITE FOR RESIDUE LEO A 201
2AC2SOFTWAREMET B:38 , PHE B:54 , TYR B:120BINDING SITE FOR RESIDUE LEO B 202
3AC3SOFTWAREMET C:38 , PHE C:54 , TYR C:120BINDING SITE FOR RESIDUE LEO C 203
4AC4SOFTWAREMET D:38 , PHE D:54 , TYR D:120BINDING SITE FOR RESIDUE LEO D 204

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:64 -A:157
2B:64 -B:157
3C:64 -C:157
4D:64 -D:157

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A2G)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.MUP_RAT28-41
 
 
 
  4A:9-22
B:9-22
C:9-22
D:9-22

(-) Exons   (0, 0)

(no "Exon" information available for 2A2G)

(-) 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:158
 aligned with MUP_RAT | P02761 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:158
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        
              MUP_RAT    20 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 177
               SCOP domains d2a2ga_ A: Major urinary protein/alpha-2u-globulin                                                                                                             SCOP domains
               CATH domains 2a2gA00 A:1-158  [code=2.40.128.20, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhh....eeeeee...hhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeee.......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhh....hhheeehhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2g A   1 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with MUP_RAT | P02761 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:158
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        
              MUP_RAT    20 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 177
               SCOP domains d2a2gb_ B: Major urinary protein/alpha-2u-globulin                                                                                                             SCOP domains
               CATH domains 2a2gB00 B:1-158  [code=2.40.128.20, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhh....eeeeee...hhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeee.......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhh....hhheeehhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2g B   1 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with MUP_RAT | P02761 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:158
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        
              MUP_RAT    20 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 177
               SCOP domains d2a2gc_ C: Major urinary protein/alpha-2u-globulin                                                                                                             SCOP domains
               CATH domains 2a2gC00 C:1-158  [code=2.40.128.20, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhh....eeeeee...hhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeee.......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhh....hhheeehhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2g C   1 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with MUP_RAT | P02761 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:158
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        
              MUP_RAT    20 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 177
               SCOP domains d2a2gd_ D: Major urinary protein/alpha-2u-globulin                                                                                                             SCOP domains
               CATH domains 2a2gD00 D:1-158  [code=2.40.128.20, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhh....eeeeee...hhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeee.......eeee...eeeeeeeee....eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhh....hhheeehhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2g D   1 EEASSTRGNLDVAKLNGDWFSIVVASNKREKIEENGSMRVFMQHIDVLENSLGFKFRIKENGECRELYLVAYKTPEDGEYFVEYDGGNTFTILKTDYDRYVMFHLINFKNGETFQLMVLYGRTKDLSSDIKEKFAKLCEAHGITRDNIIDLTKTDRCL 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A2G)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MUP_RAT | P02761)
molecular function
    GO:0005009    insulin-activated receptor activity    Combining with insulin and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    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:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0007610    behavior    The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
    GO:0071396    cellular response to lipid    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 lipid stimulus.
    GO:0006112    energy reserve metabolic process    The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0031649    heat generation    Any homeostatic process in which an organism produces heat, thereby raising its internal temperature.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0045475    locomotor rhythm    The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
    GO:0070584    mitochondrion morphogenesis    The process in which the anatomical structures of a mitochondrion are generated and organized.
    GO:0045721    negative regulation of gluconeogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis.
    GO:0061179    negative regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that decreases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0051055    negative regulation of lipid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
    GO:0010888    negative regulation of lipid storage    Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    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:0010628    positive regulation of gene expression    Any process that increases 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:0010907    positive regulation of glucose metabolic process    Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0045834    positive regulation of lipid metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    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.
cellular component
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

 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
    LEO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a2g)
 

(-) 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
  2a2g
    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
  MUP_RAT | P02761
    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
  MUP_RAT | P02761
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MUP_RAT | P027612a2u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A2G)