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(-) Description

Title :  CRYSTAL STRUCTURE OF CONJUGATED POLYKETONE REDUCTASE C1 FROM CANDIDA PARAPSILOSIS COMPLEXED WITH NADPH
 
Authors :  H. -M. Qin, A. Yamamura, T. Miyakawa, S. Maruoka, J. Ohtsuka, K. Nagata, M. Kataoka, S. Shimizu, M. Tanokura
Date :  28 Jul 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Akr Superfamily, Tim Barrel, Oxidoreductase, D-Pantoyl Lactone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. -M. Qin, A. Yamamura, T. Miyakawa, M. Kataoka, S. Maruoka, J. Ohtsuka, K. Nagata, S. Shimizu, M. Tanokura
Crystal Structure Of Conjugated Polyketone Reductase (Cpr-C1) From Candida Parapsilosis Ifo 0708 Complexed With Nadph
Proteins 2013
PubMed-ID: 23852710  |  Reference-DOI: 10.1002/PROT.24363

(-) Compounds

Molecule 1 - CONJUGATED POLYKETONE REDUCTASE C1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCPR-C1
    Organism CommonYEAST
    Organism ScientificCANDIDA PARAPSILOSIS
    Organism Taxid5480
    StrainIFO 0708

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:22 , THR A:23 , GLY A:24 , THR A:25 , LYS A:26 , ASP A:55 , TYR A:60 , LYS A:85 , HIS A:125 , SER A:160 , ASN A:161 , GLN A:183 , TYR A:211 , GLY A:212 , PRO A:213 , LEU A:214 , THR A:218 , ILE A:256 , THR A:257 , THR A:258 , THR A:259 , SER A:260 , LYS A:261 , ARG A:264 , PHE A:296 , HOH A:3112 , HOH A:3159 , HOH A:3188 , HOH A:3191 , HOH A:3195BINDING SITE FOR RESIDUE NDP A 3001
2AC2SOFTWAREGLY B:22 , THR B:23 , GLY B:24 , THR B:25 , LYS B:26 , ASP B:55 , TYR B:60 , HIS B:125 , SER B:160 , ASN B:161 , GLN B:183 , TYR B:211 , GLY B:212 , PRO B:213 , LEU B:214 , ILE B:217 , THR B:218 , ILE B:256 , THR B:257 , THR B:258 , THR B:259 , SER B:260 , LYS B:261 , ARG B:264 , PHE B:296 , HOH B:3129 , HOH B:3133 , HOH B:3147BINDING SITE FOR RESIDUE NDP B 3001
3AC3SOFTWAREGLY C:22 , THR C:23 , GLY C:24 , THR C:25 , LYS C:26 , ASP C:55 , TYR C:60 , HIS C:125 , SER C:160 , ASN C:161 , GLN C:183 , TYR C:211 , GLY C:212 , PRO C:213 , LEU C:214 , ILE C:217 , THR C:218 , ILE C:256 , THR C:257 , THR C:258 , THR C:259 , SER C:260 , LYS C:261 , ARG C:264 , HOH C:3104 , HOH C:3136 , HOH C:3168 , HOH C:3184 , HOH C:3195BINDING SITE FOR RESIDUE NDP C 3001
4AC4SOFTWAREGLY D:22 , THR D:23 , GLY D:24 , THR D:25 , LYS D:26 , ASP D:55 , TYR D:60 , LYS D:85 , HIS D:125 , SER D:160 , ASN D:161 , GLN D:183 , TYR D:211 , GLY D:212 , PRO D:213 , LEU D:214 , ILE D:217 , THR D:218 , ILE D:256 , THR D:257 , THR D:258 , THR D:259 , SER D:260 , LYS D:261 , ARG D:264 , PHE D:296 , HOH D:3113 , HOH D:3137 , HOH D:3144 , HOH D:3165BINDING SITE FOR RESIDUE NDP D 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WG6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:221 -Pro A:222
2Arg B:221 -Pro B:222
3Arg C:221 -Pro C:222
4Arg D:221 -Pro D:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WG6)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.CPRC1_CANPA145-162
 
 
 
  4A:145-162
B:145-162
C:145-162
D:145-162
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.CPRC1_CANPA145-162
 
 
 
  1A:145-162
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.CPRC1_CANPA145-162
 
 
 
  1-
B:145-162
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.CPRC1_CANPA145-162
 
 
 
  1-
-
C:145-162
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.CPRC1_CANPA145-162
 
 
 
  1-
-
-
D:145-162

(-) Exons   (0, 0)

(no "Exon" information available for 3WG6)

(-) 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:299
 aligned with CPRC1_CANPA | Q76L37 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:299
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         
          CPRC1_CANPA     6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKYD 304
               SCOP domains d3wg6a_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..eee.hhhhh.......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeee...............hhhhhhhhhhhhhh...eeeeee.....hhhhhh.hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhh.......eeeee..........hhhhhhhhh..eeeee..hhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wg6 A   6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKYD 304
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with CPRC1_CANPA | Q76L37 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:299
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         
          CPRC1_CANPA     6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKYD 304
               SCOP domains d3wg6b_ B: automated matc    hes                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..eee.hhhhh..----.hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeee...............hhhhhhhhhhhhhh...eeeeee.....hhhhhh.hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh........eeeee..........hhhhhhhhh..eeeee..hhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wg6 B   6 KEFKLSNGNKIPAVAFGTGTKYFKR----LDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKYD 304
                                    15        25    |   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295         
                                                   30   35                                                                                                                                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:298
 aligned with CPRC1_CANPA | Q76L37 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295        
          CPRC1_CANPA     6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKY 303
               SCOP domains d3wg6c_ C: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..eee.hhhhh.......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeee...............hhhhhhhhhhhhhh.....eeee.....hhhhhh.hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh.......eeeee..........hhhhhhhhh..eeeee..hhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wg6 C   6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKY 303
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295        

Chain D from PDB  Type:PROTEIN  Length:298
 aligned with CPRC1_CANPA | Q76L37 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295        
          CPRC1_CANPA     6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKY 303
               SCOP domains d3wg6d_ D: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee..eee.hhhhh.......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeee...............hhhhhhhhhhhhhh...eeeeee.....hhhhhh.hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.......eeeee..........hhhhhhhhh..eeeee..hhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wg6 D   6 KEFKLSNGNKIPAVAFGTGTKYFKRGHNDLDKQLIGTLELALRSGFRHIDGAEIYGTNKEIGIALKNVGLNRKDVFITDKYNSGNHTYDGKHSKHQNPYNALKADLEDLGLEYVDLYLIHFPYISEKSHGFDLVEAWRYLERAKNEGLARNIGVSNFTIENLKSILDANTDSIPVVNQIEFSAYLQDQTPGIVEYSQQQGILIEAYGPLGPITQGRPGPLDKVLSKLSEKYKRNEGQILLRWVLQRGILPITTTSKEERINDVLEIFDFELDKEDEDQITKVGKEKTLRQFSKEYSKY 303
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295        

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WG6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CPRC1_CANPA | Q76L37)
molecular function
    GO:0047011    2-dehydropantolactone reductase (A-specific) activity    Catalysis of the reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NADP+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0042180    cellular ketone metabolic process    The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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