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(-) Description

Title :  DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO COMPOUND 15
 
Authors :  C. G. Noble
Date :  17 Jan 16  (Deposition) - 30 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor Complex Polymerase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Yokokawa, S. Nilar, C. G. Noble, S. P. Lim, R. Rao, S. Tania, G. Wang, G. Lee, J. Hunziker, R. Karuna, U. Manjunatha, P. Y. Shi, P. W. Smith
Discovery Of Potent Non-Nucleoside Inhibitors Of Dengue Viral Rna-Dependent Rna Polymerase From A Fragment Hit Usin Structure-Based Drug Design.
J. Med. Chem. V. 59 3935 2016
PubMed-ID: 26984786  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00143

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE NS5
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1LNY1Ligand/Ion2,2'-(5-(5-(3-HYDROXYPROP-1-YN-1-YL)THIOPHEN-2-YL)-1,3-PHENYLENE)DIACETIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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
3AC3SOFTWARELEU A:511 , HIS A:512 , CYS A:709 , ARG A:729 , ARG A:737 , MET A:761 , MET A:765 , TYR A:766 , THR A:794 , SER A:796 , HIS A:798 , ALA A:799 , HIS A:800 , GLN A:802 , TRP A:803 , HOH A:1111 , HOH A:1117 , HOH A:1154binding site for residue LNY A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HMY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HMY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HMY)

(-) Exons   (0, 0)

(no "Exon" information available for 5HMY)

(-) 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:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............eeeeeee...........hhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhheeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmy A 272 NMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAADSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMPSMKRF 889
                                   281       291       301       311       321       331       341       351       361       371       381       391       401     ||422       432       442       452||     478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888 
                                                                                                                                                                 407|                               453|                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                  419                                470
   Legend:   → Mismatch (orange background)
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  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 5HMY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HMY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HMY)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hmy
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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 4hhj 4v0q 4v0r 5dto 5eiw 5f3t 5f3z 5f41 5hmw 5hmx 5hmz 5hn0 5i3p 5i3q 5iq6 5jjr 5jjs

(-) Related Entries Specified in the PDB File

5hmw 5hmx 5hmz 5hn0