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(-) Description

Title :  DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE
 
Authors :  C. G. Noble, J. Lescar
Date :  10 Oct 12  (Deposition) - 27 Feb 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Rdrp, Viral Protein, Rna-Dependent Rna Polymerase, Rna Binding, Er Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Noble, S. P. Lim, Y. L. Chen, C. W. Liew, L. Yap, J. Lescar, P. -Y. Shi
Conformational Flexibility Of The Dengue Virus Rna-Dependen Rna Polymerase Revealed By A Complex With An Inhibitor
J. Virol. V. 87 5291 2013
PubMed-ID: 23408636  |  Reference-DOI: 10.1128/JVI.00045-13

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 5
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RNA-DEPENDENT RNA POLYMERASE, UNP RESIDUES 2762-3390
    Organism Scientific: DENGUE VIRUS 3
    Organism Taxid: 11069

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1P6G1Ligand/IonHEXAETHYLENE GLYCOL
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:712 , HIS A:714 , CYS A:728 , CYS A:847BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREGLU A:437 , HIS A:441 , CYS A:446 , CYS A:449BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREGLN A:705 , HIS A:711 , HIS A:712 , TRP A:846 , HOH A:1517 , HOH A:1548 , HOH A:1603BINDING SITE FOR RESIDUE P6G A 1003
4AC4SOFTWAREASN A:635 , HIS A:637 , HOH A:1445 , HOH A:1758BINDING SITE FOR RESIDUE PEG A 1004
5AC5SOFTWAREASP A:826 , HOH A:1144 , HOH A:1642BINDING SITE FOR RESIDUE PEG A 1005
6AC6SOFTWAREPRO A:822 , TRP A:823BINDING SITE FOR RESIDUE PEG A 1006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HHJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HHJ)

(-) 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:588
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeeeeee.........eehhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hhj A 272 NMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNASAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGKRGSRAIWYMWLGVRYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM 883
                                   281       291       301       311       321       331       341       351       361       371       381       391       401    || 424       434       444       454  ||   475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875        
                                                                                                                                                                406|                                  457|                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                 420                                   469
   Legend:   → Mismatch (orange background)
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    → 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 4HHJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hhj
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  Q6DLV0_9FLAV | Q6DLV0
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6DLV0_9FLAV | Q6DLV0: 3j6s 3j6t 3j6u
UniProtKB/TrEMBL
        Q6DLV0_9FLAV | Q6DLV0: 2j7u 2j7w 3vws 4c11 4v0q 4v0r 5dto 5eiw 5f3t 5f3z 5f41 5hmw 5hmx 5hmy 5hmz 5hn0 5i3p 5i3q 5iq6 5jjr 5jjs

(-) Related Entries Specified in the PDB File

3vws THE SAME PROTEIN WITH AN INHIBITOR