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(-) Description

Title :  PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE WITH QUINOLINE INHIBITOR
 
Authors :  V. Goncalves, J. A. Brannigan, D. Whalley, K. H. Ansell, B. Saxty, A. A. H A. J. Wilkinson, E. W. Tate, R. J. Leatherbarrow
Date :  24 Nov 11  (Deposition) - 27 Jun 12  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Transferase, Malaria (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Goncalves, J. A. Brannigan, D. Whalley, K. H. Ansell, B. Saxty, A. A. Holder, A. J. Wilkinson, E. W. Tate, R. J. Leatherbarrow
Discovery Of Plasmodium Vivax N-Myristoyltransferase Inhibitors: Screening, Synthesis, And Structural Characterization Of Their Binding Mode.
J. Med. Chem. V. 55 3578 2012
PubMed-ID: 22439843  |  Reference-DOI: 10.1021/JM300040P

(-) Compounds

Molecule 1 - GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
    ChainsA, B, C
    EC Number2.3.1.97
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPLYSS
    Expression System VectorPET28
    Expression System Vector TypePLASMID
    FragmentRESIDUES 27-410
    Organism ScientificPLASMODIUM VIVAX
    Organism Taxid5855
    Other DetailsSYNTHETIC GENE
    SynonymN-MRISTOYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
19MT3Ligand/Ion3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE
2CL3Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION
4NHW3Ligand/Ion2-OXOPENTADECYL-COA
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
19MT1Ligand/Ion3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
19MT1Ligand/Ion3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
19MT1Ligand/Ion3-(3-BUTYL-6-METHOXY-2-METHYL-QUINOLIN-4-YL)SULFANYLPROPANENITRILE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:96 , GLU A:97 , ASP A:98 , PHE A:103 , PHE A:105 , TYR A:211 , HIS A:213 , PHE A:226 , SER A:319 , LEU A:330 , TYR A:334 , ASN A:365BINDING SITE FOR RESIDUE 9MT A1000
02AC2SOFTWARETYR A:28 , LYS A:29 , PHE A:30 , TRP A:31 , ASN A:94 , TYR A:95 , VAL A:96 , ASN A:161 , PHE A:162 , LEU A:163 , CYS A:164 , VAL A:165 , ARG A:170 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , ALA A:175 , PRO A:176 , THR A:183 , ILE A:186 , ASN A:187 , TRP A:192 , ALA A:194 , THR A:197 , LEU A:202 , TYR A:393 , MG A:1412 , HOH A:2002 , HOH A:2005 , HOH A:2303 , HOH A:2311 , HOH A:2569 , HOH A:2570 , HOH A:2571 , HOH A:2572 , HOH A:2573 , HOH A:2574BINDING SITE FOR RESIDUE NHW A1001
03AC3SOFTWARELYS A:180 , THR A:247 , LEU A:248 , ARG A:358BINDING SITE FOR RESIDUE CL A1411
04AC4SOFTWARELEU A:169 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , NHW A:1001BINDING SITE FOR RESIDUE MG A1412
05AC5SOFTWAREVAL B:96 , GLU B:97 , ASP B:98 , PHE B:103 , PHE B:105 , TYR B:211 , HIS B:213 , PHE B:226 , SER B:319 , TYR B:334 , ASN B:365BINDING SITE FOR RESIDUE 9MT B1000
06AC6SOFTWAREASP B:27 , TYR B:28 , LYS B:29 , PHE B:30 , TRP B:31 , ASN B:94 , TYR B:95 , VAL B:96 , ASN B:161 , PHE B:162 , LEU B:163 , CYS B:164 , VAL B:165 , ARG B:170 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , ALA B:175 , PRO B:176 , THR B:183 , TRP B:192 , GLN B:193 , TYR B:196 , THR B:197 , ALA B:198 , LEU B:202 , TYR B:393 , MG B:1413 , HOH B:2003 , HOH B:2270 , HOH B:2274 , HOH B:2275 , HOH B:2515 , HOH B:2516 , HOH B:2517 , HOH B:2518 , HOH B:2519 , HOH B:2520BINDING SITE FOR RESIDUE NHW B1001
07AC7SOFTWAREARG A:210 , ARG B:210 , HOH B:2521BINDING SITE FOR RESIDUE SO4 B1411
08AC8SOFTWARELYS B:180 , THR B:247 , LEU B:248 , ARG B:358BINDING SITE FOR RESIDUE CL B1412
09AC9SOFTWARELEU B:169 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , NHW B:1001BINDING SITE FOR RESIDUE MG B1413
10BC1SOFTWAREVAL C:96 , GLU C:97 , ASP C:98 , PHE C:103 , PHE C:105 , TYR C:211 , HIS C:213 , SER C:319 , LEU C:330 , TYR C:334 , ASN C:365BINDING SITE FOR RESIDUE 9MT C1000
11BC2SOFTWARETYR C:28 , LYS C:29 , PHE C:30 , TRP C:31 , ASN C:94 , TYR C:95 , VAL C:96 , ASN C:161 , PHE C:162 , LEU C:163 , CYS C:164 , VAL C:165 , ARG C:170 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , ALA C:175 , PRO C:176 , THR C:183 , ILE C:186 , TRP C:192 , ALA C:194 , TYR C:196 , THR C:197 , LEU C:202 , TYR C:393 , MG C:1412 , HOH C:2002 , HOH C:2003 , HOH C:2224 , HOH C:2231 , HOH C:2436 , HOH C:2437 , HOH C:2438 , HOH C:2439 , HOH C:2440BINDING SITE FOR RESIDUE NHW C1001
12BC3SOFTWARELYS C:180 , THR C:247 , LEU C:248 , ARG C:358BINDING SITE FOR RESIDUE CL C1411
13BC4SOFTWARELEU C:169 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , NHW C:1001BINDING SITE FOR RESIDUE MG C1412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A95)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:203 -Lys A:204
2Pro B:203 -Lys B:204
3Pro C:203 -Lys C:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A95)

(-) Exons   (0, 0)

(no "Exon" information available for 4A95)

(-) 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:384
 aligned with A5K1A2_PLAVS | A5K1A2 from UniProtKB/TrEMBL  Length:410

    Alignment length:384
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    
         A5K1A2_PLAVS    27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhh.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a95 A  27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    

Chain B from PDB  Type:PROTEIN  Length:384
 aligned with A5K1A2_PLAVS | A5K1A2 from UniProtKB/TrEMBL  Length:410

    Alignment length:384
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    
         A5K1A2_PLAVS    27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a95 B  27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    

Chain C from PDB  Type:PROTEIN  Length:366
 aligned with A5K1A2_PLAVS | A5K1A2 from UniProtKB/TrEMBL  Length:410

    Alignment length:384
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    
         A5K1A2_PLAVS    27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeee........eeeeeeeee.hhhhhhhh.------------------..........ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeee....eeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a95 C  27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIG------------------VEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        |-         -       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    
                                                                                                                                                                                                                                225                244                                                                                                                                                                      

   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 4A95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A95)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (A5K1A2_PLAVS | A5K1A2)
molecular function
    GO:0004379    glycylpeptide N-tetradecanoyltransferase activity    Catalysis of the reaction: tetradecanoyl-CoA + glycyl-peptide = CoA + N-tetradecanoylglycyl-peptide.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006499    N-terminal protein myristoylation    The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.

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 Related Entries

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

UniProtKB/TrEMBL
        A5K1A2_PLAVS | A5K1A22ync 2ynd 2yne 4b10 4b11 4b12 4b13 4b14 4bbh 4c68 4cae 4caf 4ufv 4ufw 4ufx 5g1z 5g22

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