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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NOROVIRUS RNA-DEPENDENT RNA-POLYMERASE BOUND TO THE INHIBITOR PPNDS
 
Authors :  M. Milani, D. Tarantino, E. Mastrangelo, R. Croci
Date :  17 Jul 13  (Deposition) - 12 Feb 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,R
Keywords :  Rna-Dependent-Rna-Polymerase, Rdrp-Inhibotir Complex, Viral Protein- Replication Inhibitor-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tarantino, M. Pezzullo, E. Mastrangelo, R. Croci, J. Rohayem, I. Robel, M. Bolognesi, M. Milani
Naphthalene-Sulfonate Inhibitors Of Human Norovirus Rna-Dependent Rna-Polymerase.
Antiviral Res. V. 102 23 2014
PubMed-ID: 24316032  |  Reference-DOI: 10.1016/J.ANTIVIRAL.2013.11.016

(-) Compounds

Molecule 1 - RNA-DEPENDENT RNA-POLYMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: NOROVIRUS
    Organism Taxid: 142786
 
Molecule 2 - 5'-R(P*GP*G)-3'
    Chains: R
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
120V4Ligand/Ion3-[(E)-{4-FORMYL-5-HYDROXY-6-METHYL-3-[(PHOSPHONOOXY)METHYL]PYRIDIN-2-YL}DIAZENYL]-7-NITRONAPHTHALENE-1,5-DISULFONIC ACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:146 , GLU A:323 , VAL A:324 , THR A:325 , ASN A:326 , ASP A:354 , LYS A:357 , 20V A:602BINDING SITE FOR RESIDUE 20V A 601
2AC2SOFTWAREPRO A:122 , HIS A:123 , ASP A:142 , GLN A:143 , LYS A:357 , 20V A:601BINDING SITE FOR RESIDUE 20V A 602
3AC3SOFTWARELYS A:166 , ASP A:167 , GLU A:168 , ARG A:392 , LEU A:406 , SER A:410 , ILE A:411 , ARG A:413 , GLN A:414 , ARG A:419 , GLN A:439 , LEU A:443 , ASP A:507 , GLU A:510BINDING SITE FOR RESIDUE 20V A 603
4AC4SOFTWAREARG A:252 , ILE A:463 , ALA A:464 , LYS A:467 , HOH A:789BINDING SITE FOR RESIDUE 20V A 604
5AC5SOFTWAREASP A:240 , ASP A:344 , GLU A:345 , THR A:389BINDING SITE FOR RESIDUE MG A 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LQ3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:121 -Pro A:122
2Val A:509 -Glu A:510

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4LQ3)

(-) 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:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeeee.........eeeee...........ee..............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeee...eehhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh....................ee..eeeeee..eeeeeehhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lq3 A   6 GTYCGAPILGPGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFTQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEGGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFKISINEPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGMDYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE 510
                                    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||     307       317       327       337       347       357       367     ||380       390       400       410       420       430|      443       453       463    || 475       485       495       505     
                                                                                                                                                                                                                                                                                                                            296|                                                                       373|                                                  430|                               468| ||                                    
                                                                                                                                                                                                                                                                                                                             299                                                                        377                                                   434                                470 ||                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   472|                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    474                                    


Chain R from PDB  Type:RNA  Length:2
                                  
                 4lq3 R   1 GG   2
   Legend:   → Mismatch (orange background)
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  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 4LQ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LQ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LQ3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:121 - Pro A:122   [ RasMol ]  
    Val A:509 - Glu A:510   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q2N379_9CALI | Q2N379: 4lq9

(-) Related Entries Specified in the PDB File

4lq9