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(-) Description

Title :  X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX
 
Authors :  Y. Xu, P. D. Carr, J. M. Guss, D. L. Ollis
Date :  26 Nov 97  (Deposition) - 16 Mar 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoprotein, Bikunin, Trypstatin, Urinary Trypsin Inhibitor, Uronic- Acid-Rich Protein, Serine Protease Inhibitor (Kunitz Type), Glycosylated Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Xu, P. D. Carr, J. M. Guss, D. L. Ollis
The Crystal Structure Of Bikunin From The Inter-Alpha-Inhibitor Complex: A Serine Protease Inhibitor With Two Kunitz Domains.
J. Mol. Biol. V. 276 955 1998
PubMed-ID: 9566199  |  Reference-DOI: 10.1006/JMBI.1997.1582

(-) Compounds

Molecule 1 - BIKUNIN
    ChainsA
    FragmentDOMAIN II,78 - 133
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SecretionURINE
    SynonymMINGIN, URINARY TRYPSIN INHIBITOR, HI30, TRYPSTATIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:30 , ASN A:45 , THR A:47 , SER A:48BINDING SITE FOR RESIDUE NAG A 148
2AC2SOFTWAREVAL A:87 , ARG A:88 , GLY A:89BINDING SITE FOR RESIDUE SO4 A 149
3AC3SOFTWAREMET A:38 , SER A:40 , GLN A:55 , LYS A:104 , LYS A:106BINDING SITE FOR RESIDUE SO4 A 150

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:76
2A:35 -A:59
3A:51 -A:72
4A:82 -A:132
5A:91 -A:115
6A:107 -A:128

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BIK)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.AMBP_HUMAN231-281
287-337
  2A:26-76
A:82-132
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.AMBP_HUMAN259-277
315-333
  2A:54-72
A:110-128

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002651321ENSE00000926885chr9:116840752-116840373380AMBP_HUMAN1-39390--
1.3ENST000002651323ENSE00000926884chr9:116839020-116838878143AMBP_HUMAN40-87480--
1.4bENST000002651324bENSE00000926883chr9:116837316-11683724077AMBP_HUMAN87-113270--
1.5bENST000002651325bENSE00000926882chr9:116836432-116836316117AMBP_HUMAN113-152400--
1.6bENST000002651326bENSE00000926881chr9:116835306-116835205102AMBP_HUMAN152-186350--
1.7ENST000002651327ENSE00000983921chr9:116832025-11683197947AMBP_HUMAN186-201160--
1.8ENST000002651328ENSE00000983922chr9:116825038-11682495782AMBP_HUMAN202-229280--
1.9bENST000002651329bENSE00000983923chr9:116823871-116823704168AMBP_HUMAN229-285571A:25-8056
1.10aENST0000026513210aENSE00000983924chr9:116823378-116823205174AMBP_HUMAN285-343591A:80-13455
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:110
 aligned with AMBP_HUMAN | P02760 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:110
                                   239       249       259       269       279       289       299       309       319       329       339
           AMBP_HUMAN   230 SCQLGYSAGPCMGMTSRYFYNGTSMACETFQYGGCMGNGNNFVTEKECLQTCRTVAACNLPIVRGPCRAFIQLWAFDAVKGKCVLFPYGGCQGNGNKFYSEKECREYCGV 339
               SCOP domains d1bika1 A:25-78                                       d1bika2 A:79-134                                         SCOP domains
               CATH domains 1bikA00 A:25-134 Factor Xa Inhibitor                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee....eeeeeee............hhhhhhhh..hhhhh...........eeeeeee....eeeeeee............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -BPTI_KUNITZ_2  PDB: A:26-76 UniProt: 231-281       -----BPTI_KUNITZ_2  PDB: A:82-132 UniProt: 287-337      -- PROSITE (1)
                PROSITE (2) -----------------------------BPTI_KUNITZ_1      -------------------------------------BPTI_KUNITZ_1      ------ PROSITE (2)
           Transcript 1 (1) -------------------------------------------------------Exon 1.10a  PDB: A:80-134 UniProt: 285-343 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) Exon 1.9b  PDB: A:25-80 UniProt: 229-285 [INCOMPLETE]   ------------------------------------------------------ Transcript 1 (2)
                 1bik A  25 SCQLGYSAGPCMGMTSRYFYNGTSMACETFQYGGCMGNGNNFVTEKECLQTCRTVAACNLPIVRGPCRAFIQLWAFDAVKGKCVLFPYGGCQGNGNKFYSEKECREYCGV 134
                                    34        44        54        64        74        84        94       104       114       124       134

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BIK)

(-) 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 | P027603qkg 4es7 4u30

(-) Related Entries Specified in the PDB File

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