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(-) Description

Title :  IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
 
Authors :  J. Sandmark, M. Althage, G. M. K. Andersson, T. Antonsson, S. Blaho, C. B J. Bostrom, Y. Chen, A. Dahlen, P. O. Eriksson, E. Evertsson, T. Fex, O. Fjellstrom, D. Gustafsson, C. Hallberg, R. Hicks, E. Jarkvist, C. J I. Kalies, D. Kang, B. Svalstedt Karlsson, F. Kartberg, A. Legnehed, A. M. Lindqvist, S. A. Martinsson, A. Moberg, A. U. Petersson, M. Ridde A. Thelin, A. Tigerstrom, J. Vinblad, B. Xu, W. Knecht
Date :  25 Jun 13  (Deposition) - 09 Jul 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Cardiovascular Disease, Optical Biosensors (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Sandmark, M. Althage, G. M. K. Andersson, T. Antonsson, S. Blaho, C. Bodin, J. Bostrom, Y. Chen, A. Dahlen, P. O. Eriksson, E. Evertsson, T. Fex, O. Fjellstrom, D. Gustafsson, C. Hallberg, R. Hicks, E. Jarkvist, C. Johansson, I. Kalies, D. Kang, B. Svalstedt Karlsson F. Kartberg, A. Legnehed, A. M. Lindqvist, S. A. Martinsson, A. Moberg A. U. Petersson, M. Ridderstrom, A. Thelin, A. Tigerstrom, J. Vinblad B. Xu, W. Knecht
Small Molecules Used To Decipher The Pathophysiological Roles Of The Kringle Domains Kiv-7, - 10 And Kv Of Apolipoprotein(A)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - APOLIPOPROTEIN(A)
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZALPHA
    Expression System StrainX-33
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentKRINGLE IV-10, RESIDUES 4123-4201
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPO(A), LP(A)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15C32Ligand/Ion4-(AMINOMETHYL)-N-(BENZENESULFONYL)CYCLOHEXANECARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15C31Ligand/Ion4-(AMINOMETHYL)-N-(BENZENESULFONYL)CYCLOHEXANECARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15C31Ligand/Ion4-(AMINOMETHYL)-N-(BENZENESULFONYL)CYCLOHEXANECARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , GLN A:34 , ARG A:35 , ASP A:55 , ASP A:57 , TRP A:62 , PHE A:64 , ARG A:71 , TRP A:72 , ASP B:67 , PRO B:68 , SER B:69BINDING SITE FOR RESIDUE 5C3 A1081
2AC2SOFTWAREASP A:67 , PRO A:68 , SER A:69 , HIS B:33 , GLN B:34 , ARG B:35 , ASP B:55 , ASP B:57 , TRP B:62 , ARG B:71 , TRP B:72BINDING SITE FOR RESIDUE 5C3 B1081

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:1 -A:80
2A:22 -A:63
3A:51 -A:75
4B:1 -B:80
5B:22 -B:63
6B:51 -B:75

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:29 -Pro A:30
2Thr B:29 -Pro B:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047299M4187TAPOA_HUMANPolymorphism1801693A/BM66T
2UniProtVAR_006633W4193RAPOA_HUMANUnclassified  ---A/BW72R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047299M4187TAPOA_HUMANPolymorphism1801693AM66T
2UniProtVAR_006633W4193RAPOA_HUMANUnclassified  ---AW72R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047299M4187TAPOA_HUMANPolymorphism1801693BM66T
2UniProtVAR_006633W4193RAPOA_HUMANUnclassified  ---BW72R

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KRINGLE_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
  2-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
A:50-63
B:50-63
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KRINGLE_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:50-63
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KRINGLE_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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
B:50-63
-

(-) Exons   (0, 0)

(no "Exon" information available for 4BV5)

(-) Sequences/Alignments

Asymmetric 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:78
 aligned with APOA_HUMAN | P08519 from UniProtKB/Swiss-Prot  Length:4548

    Alignment length:78
                                  4133      4143      4153      4163      4173      4183      4193        
          APOA_HUMAN   4124 CYHGNGQSYRGTFSTTVTGRTCQSWSSMTPHRHQRTPENYPNDGLTMNYCRNPDADTGPWCFTMDPSIRWEYCNLTRC 4201
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................................................eee.......eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------T-----R-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------KRINGLE_1    ----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                4bv5 A    1 CYHGNGQSYRGTFSTTVTGRTCQSWSSMTPHRHQRTPENYPNDGLTMNYCRNPDADTGPWCFTMDPSIRWEYCALTRC   80
                                    10        20        30    ||  41        51      ||62        72        
                                                             35|                   58|                    
                                                              37                    60                    

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with APOA_HUMAN | P08519 from UniProtKB/Swiss-Prot  Length:4548

    Alignment length:78
                                  4133      4143      4153      4163      4173      4183      4193        
          APOA_HUMAN   4124 CYHGNGQSYRGTFSTTVTGRTCQSWSSMTPHRHQRTPENYPNDGLTMNYCRNPDADTGPWCFTMDPSIRWEYCNLTRC 4201
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................................................eee.......eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------T-----R-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------KRINGLE_1    ----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                4bv5 B    1 CYHGNGQSYRGTFSTTVTGRTCQSWSSMTPHRHQRTPENYPNDGLTMNYCRNPDADTGPWCFTMDPSIRWEYCALTRC   80
                                    10        20        30    ||  41        51      ||62        72        
                                                             35|                   58|                    
                                                              37                    60                    

   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  (0, 0)

(no "SCOP Domain" information available for 4BV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BV5)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P085191i71 1jfn 1kiv 2feb 3kiv 4bv7 4bvc 4bvd 4bvv 4bvw 4kiv

(-) Related Entries Specified in the PDB File

4bv7 IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvc IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvd IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvv IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.
4bvw IDENTIFICATION OF SMALL MOLECULE INHIBITORS SELECTIVE FOR APO(A) KRINGLES KIV-7, KIV-10 AND KV.