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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-1-MICROGLOBULIN AT 2.3 A RESOLUTION
 
Authors :  W. Meining, A. Skerra
Date :  01 Feb 11  (Deposition) - 08 Feb 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Binding Protein, Bound Chromophore, Human Plasma, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Meining, A. Skerra
The Crystal Structure Of Human Alpha(1)-Microglobulin Reveals A Potential Haem-Binding Site.
Biochem. J. V. 445 175 2012
PubMed-ID: 22512701  |  Reference-DOI: 10.1042/BJ20120448

(-) Compounds

Molecule 1 - PROTEIN AMBP
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPA1M2
    Expression System StrainK-12
    Expression System Taxid83333
    Expression System Vector TypePLASMID
    FragmentLIPOCALIN
    GeneAMBP, HCP, ITIL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-1-MICROGLOBULIN, PROTEIN HC, ALPHA-1 MICROGLYCOPROTEIN, COMPLEX-FORMING GLYCOPROTEIN HETEROGENEOUS IN CHARGE, INTER-ALPHA-TRYPSIN INHIBITOR LIGHT CHAIN, ITI-LC, BIKUNIN, EDC1, HI-30, URONIC-ACID-RICH PROTEIN, TRYPSTATIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:122 , HIS A:123 , HOH A:196 , HOH A:197 , HOH A:198 , HOH A:199BINDING SITE FOR RESIDUE NI A 194
2AC2SOFTWARETRP A:67 , GLY A:70 , CYS A:72 , VAL A:170 , PRO A:171 , HOH A:220BINDING SITE FOR RESIDUE GOL A 195

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:72 -A:169

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.AMBP_HUMAN34-47  1A:15-28

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002651321ENSE00000926885chr9:116840752-116840373380AMBP_HUMAN1-39391A:8-2013
1.3ENST000002651323ENSE00000926884chr9:116839020-116838878143AMBP_HUMAN40-87481A:21-6848
1.4bENST000002651324bENSE00000926883chr9:116837316-11683724077AMBP_HUMAN87-113271A:68-9427
1.5bENST000002651325bENSE00000926882chr9:116836432-116836316117AMBP_HUMAN113-152401A:94-13340
1.6bENST000002651326bENSE00000926881chr9:116835306-116835205102AMBP_HUMAN152-186351A:133-16735
1.7ENST000002651327ENSE00000983921chr9:116832025-11683197947AMBP_HUMAN186-201161A:167-1715
1.8ENST000002651328ENSE00000983922chr9:116825038-11682495782AMBP_HUMAN202-229280--
1.9bENST000002651329bENSE00000983923chr9:116823871-116823704168AMBP_HUMAN229-285570--
1.10aENST0000026513210aENSE00000983924chr9:116823378-116823205174AMBP_HUMAN285-343590--
1.11ENST0000026513211ENSE00001034290chr9:116822550-116822407144AMBP_HUMAN343-352100--

(-) 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:164
 aligned with AMBP_HUMAN | P02760 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:164
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
           AMBP_HUMAN    27 DNIQVQENFNISRIYGKWYNLAIGSTCPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSIFTMADRGECVP 190
               SCOP domains d3qkga_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhheeeeeeeeee.hhhhhhhh.....eeeeeee.....eeeeeeeee....eeeeeeeeee.....eeeeee....eeeeeeeeee....eeeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhh......eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1     Exon 1.3  PDB: A:21-68 UniProt: 40-87           -------------------------Exon 1.5b  PDB: A:94-133                ---------------------------------1.7   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4b  PDB: A:68-94    --------------------------------------Exon 1.6b  PDB: A:133-167          ---- Transcript 1 (2)
                 3qkg A   8 DNIQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYEKTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSIFTMADRGECVP 171
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    

   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 3QKG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMBP_HUMAN | P02760)
molecular function
    GO:0019862    IgA binding    Interacting selectively and non-covalently with an immunoglobulin of an IgA isotype.
    GO:0019855    calcium channel inhibitor activity    Stops, prevents, or reduces the activity of a calcium channel.
    GO:0046904    calcium oxalate binding    Interacting selectively and non-covalently with calcium oxalate, CaC2O4, a salt of oxalic acid. In animals, it may be excreted in urine or retained in the form of urinary calculi.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0042167    heme catabolic process    The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046329    negative regulation of JNK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0050777    negative regulation of immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    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:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMBP_HUMAN | P027601bik 4es7 4u30

(-) Related Entries Specified in the PDB File

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