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(-) Description

Title :  CRYSTAL STRUCTURES AND FUNCTIONAL ANALYSIS OF MURINE NOROVIRUS RNA-DEPENDENT RNA POLYMERASE
 
Authors :  K. H. Kim, J. H. Lee, I. Alam, Y. Park, S. Kang
Date :  02 Jun 10  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Rna-Dependent Rna Polymerase, Murine Norovirus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. H. Kim, J. H. Lee, I. Alam, Y. Park, S. Kang
Crystal Structures And Functional Analysis Of Murine Norovirus Rna-Dependent Rna Polymerase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RNA DEPENDENT RNA POLYMERASE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainER2566
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificMURINE NOROVIRUS 1
    Organism Taxid223997
    SynonymRDRP

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:410 , ARG A:411 , HIS A:453BINDING SITE FOR RESIDUE SO4 A 3
2AC2SOFTWAREGLY B:51 , SER B:52 , SER B:61 , LEU B:62BINDING SITE FOR RESIDUE SO4 B 1
3AC3SOFTWAREARG B:408BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:9 -Gly A:10
2Tyr A:124 -Pro A:125
3Gly A:380 -Pro A:381
4Gly A:491 -Thr A:492
5Ser B:9 -Gly B:10
6Tyr B:124 -Pro B:125
7Gly B:380 -Pro B:381
8Gly B:491 -Thr B:492
9Ser C:9 -Gly C:10
10Tyr C:124 -Pro C:125
11Gly C:380 -Pro C:381
12Gly C:491 -Thr C:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NAH)

(-) Exons   (0, 0)

(no "Exon" information available for 3NAH)

(-) 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:486
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:486
                                  1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613      1623      1633      1643      1653      1663      
        Q80J95_9CALI   1184 RPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT 1669
               SCOP domains d3naha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...eee..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...ee..................ee..eeeeee..eeeee.hhhhhhhhhheeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3nah A    7 RPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT  492
                                    16        26        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       416       426       436       446       456       466       476       486      

Chain B from PDB  Type:PROTEIN  Length:485
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:485
                                  1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664     
        Q80J95_9CALI   1185 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT 1669
               SCOP domains d3nahb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh.......................ee..eeee......eee.hhhhhhhhhheeeeeee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nah B    8 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT  492
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487     

Chain C from PDB  Type:PROTEIN  Length:485
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:485
                                  1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664     
        Q80J95_9CALI   1185 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT 1669
               SCOP domains d3nahc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------RdRP_1-3nahC01 C:24-490                                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (1)
           Pfam domains (2) ----------------RdRP_1-3nahC02 C:24-490                                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (2)
           Pfam domains (3) ----------------RdRP_1-3nahC03 C:24-490                                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (3)
         Sec.struct. author ...ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeeee..ee.hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh.......................ee..eeeeee..eeeee.hhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nah C    8 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGT  492
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487     

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: RdRP (210)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q80J95_9CALI | Q80J95)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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.
biological process
    GO:0044419    interspecies interaction between organisms    Any process in which an organism has an effect on an organism of a different species.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.

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 Related Entries

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

UniProtKB/TrEMBL
        Q80J95_9CALI | Q80J952m4g 2mcd 2mch 3nai 3qid 3sfg 3sfu 3upf 3uqs 3ur0 4ash 4nru 4o4r 4x2v 4x2w 4x2x 4x2y

(-) Related Entries Specified in the PDB File

1sh0 HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE
2b43 HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE
3bsn HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE IN COMPLEX WITH NCT
3bso HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE IN COMPLEX WITH CTP
3h5x HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE IN COMPLEX WITH ACT
3h5y HUMAN NOROVIRUS RNA DEPENDENT RNA POLYMERASE IN COMPLEX WITH CTP
3nai