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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV TYPE 7: INSIGHTS INTO LIGAND BINDING
 
Authors :  Q. Ye, M. N. Rahman, M. L. Koschinsky, Z. Jia
Date :  07 Mar 01  (Deposition) - 13 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Alipoprotein(A), Kringle, Protein-Ligand Interaction, Lysine Binding, Crystal Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Ye, M. N. Rahman, M. L. Koschinsky, Z. Jia
High-Resolution Crystal Structure Of Apolipoprotein(A) Kringle Iv Type 7: Insights Into Ligand Binding.
Protein Sci. V. 10 1124 2001
PubMed-ID: 11369850  |  Reference-DOI: 10.1110/PS.01701
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOLIPOPROTEIN(A)
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRECOMBINANT KRINGLE IV TYPE 7 (RESIDUES 3781- 3863)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPO(A)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:26 , ARG A:35 , TYR A:62 , ARG A:69 , PRO A:79 , VAL A:80 , HOH A:126 , HOH A:133 , HOH A:157 , HOH A:201 , HOH A:213BINDING SITE FOR RESIDUE SO4 A 300

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:1 -A:78
2A:22 -A:61
3A:50 -A:73

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:29 -Pro A:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I71)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KRINGLE_2PS50070 Kringle domain profile.APOA_HUMAN27-105
141-219
255-333
369-447
483-561
597-675
711-789
825-903
939-1017
1053-1131
1167-1245
1281-1359
1395-1473
1509-1587
1623-1701
1737-1815
1851-1929
1965-2043
2079-2157
2193-2271
2307-2385
2421-2499
2535-2613
2649-2727
2763-2841
2877-2955
2991-3069
3105-3183
3219-3297
3333-3411
3447-3525
3561-3639
3675-3753
3781-3859
3895-3973
4009-4087
4123-4201
4227-4307
  1-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
A:0-78
-
-
-
-
2KRINGLE_1PS00021 Kringle domain signature.APOA_HUMAN76-88
190-202
304-316
418-430
532-544
646-658
760-772
874-886
988-1000
1102-1114
1216-1228
1330-1342
1444-1456
1558-1570
1672-1684
1786-1798
1900-1912
2014-2026
2128-2140
2242-2254
2356-2368
2470-2482
2584-2596
2698-2710
2812-2824
2926-2938
3040-3052
3154-3166
3268-3280
3382-3394
3496-3508
3610-3622
3724-3736
3830-3842
3944-3956
4058-4070
4172-4184
4277-4290
  1-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
A:49-61
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1I71)

(-) 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:83
 aligned with APOA_HUMAN | P08519 from UniProtKB/Swiss-Prot  Length:4548

    Alignment length:83
                                  3790      3800      3810      3820      3830      3840      3850      3860   
          APOA_HUMAN   3781 DCYHGDGQSYRGSFSTTVTGRTCQSWSSMTPHWHQRTTEYYPNGGLTRNYCRNPDAEIRPWCYTMDPSVRWEYCNLTQCPVME 3863
               SCOP domains d1i71a_ A: Apolipoprotein A                                                         SCOP domains
               CATH domains 1i71A00 A:0-82 Plasminogen Kringle 4                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........................................................eee.......eee...ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) KRINGLE_2  PDB: A:0-78 UniProt: 3781-3859                                      ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------KRINGLE_1    --------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------- Transcript
                1i71 A    0 DCYHGDGQSYRGSFSTTVTGRTCQSWSSMTPHWHQRTTEYYPNGGLTRNYCRNPDAEIRPWCYTMDPSVRWEYCNLTQCPVME   82
                                     9        19        29        39        49        59        69        79   

   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I71)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APOA_HUMAN | P08519)
molecular function
    GO:0034185    apolipoprotein binding    Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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: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:0034358    plasma lipoprotein particle    A spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Plasma lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood or lymph.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APOA_HUMAN | P085191jfn 1kiv 2feb 3kiv 4bv5 4bv7 4bvc 4bvd 4bvv 4bvw 4kiv

(-) Related Entries Specified in the PDB File

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