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(-) Description

Title :  DENGUE 3 NS5 PROTEIN WITH COMPOUND 29
 
Authors :  J. Lescar, A. El Sahili
Date :  25 Apr 16  (Deposition) - 06 Jul 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Rdrp, Dengue, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Lim, C. G. Noble, C. C. Seh, T. S. Soh, A. El Sahili, G. K. Chan, J. Lescar, R. Arora, T. Benson, S. Nilar, U. Manjunatha, K. F. Wan, H. Dong, X. Xie, P. Y. Shi, F. Yokokawa
Potent Allosteric Dengue Virus Ns5 Polymerase Inhibitors: Mechanism Of Action And Resistance Profiling
Plos Pathog. V. 12 05737 2016
PubMed-ID: 27500641  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005737

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2494-3385
    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  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
168E1Ligand/Ion5-[5-(3-HYDROXYPROP-1-YN-1-YL)THIOPHEN-2-YL]-4-METHOXY-2-METHYL-N-[(QUINOLIN-8-YL)SULFONYL]BENZAMIDE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
6ZN2Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:437 , HIS A:441 , CYS A:446 , CYS A:449binding site for residue ZN A 1001
02AC2SOFTWAREHIS A:712 , HIS A:714 , CYS A:728 , CYS A:847binding site for residue ZN A 1002
03AC3SOFTWARESER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:83 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , HIS A:110 , GLU A:111 , LYS A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , HOH A:1115 , HOH A:1149 , HOH A:1427binding site for residue SAH A 1003
04AC4SOFTWAREMET A:340 , LEU A:511 , HIS A:512 , CYS A:709 , SER A:710 , HIS A:711 , ARG A:729 , ARG A:737 , MET A:761 , MET A:765 , THR A:794 , SER A:796 , HIS A:798 , HIS A:800 , GLN A:802 , TRP A:803 , HOH A:1139 , HOH A:1216 , HOH A:1296binding site for residue 68E A 1004
05AC5SOFTWARELYS A:14 , LEU A:17 , ASN A:18 , PRO A:152binding site for residue EDO A 1005
06AC6SOFTWAREASP A:533 , ASP A:664 , HOH A:1130 , HOH A:1143 , HOH A:1221 , HOH A:1263binding site for residue MG A 1006
07AC7SOFTWAREASN A:492 , HOH A:1217binding site for residue EDO A 1007
08AC8SOFTWARELYS A:401 , TRP A:477 , ARG A:481 , VAL A:603 , EDO A:1009 , HOH A:1217binding site for residue PEG A 1008
09AC9SOFTWAREASN A:452 , GLY A:601 , PEG A:1008 , HOH A:1109binding site for residue EDO A 1009
10AD1SOFTWAREGLY A:32 , ILE A:33 , ARG A:206 , PRO A:208 , LEU A:237 , ARG A:241 , HOH A:1153 , HOH A:1285binding site for residue PEG A 1010
11AD2SOFTWAREARG A:499 , LYS A:656 , HOH A:1119 , HOH A:1154binding site for residue EDO A 1011
12AD3SOFTWAREVAL A:66 , ASN A:69 , ILE A:72 , GLU A:296 , EDO A:1013 , HOH A:1138binding site for residue EDO A 1012
13AD4SOFTWAREILE A:72 , LYS A:95 , LYS A:96 , ASN A:297 , PRO A:298 , EDO A:1012 , HOH A:1147binding site for residue EDO A 1013
14AD5SOFTWAREGLU A:35 , VAL A:36 , ASP A:37 , ARG A:38 , THR A:39 , LYS A:42 , ARG A:57binding site for residue PEG A 1014

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JJR)

(-) 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:845
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhh.........hhhhhhhhhhhh......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eeee..................hhhhhhhhhhhhhhhh...............eeeeeee...........hhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhh.hhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jjr A   7 ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTWDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGSRAIWYMWLGVRYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM 883
                                    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       419       429       439       449     ||473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       748       758       768       778       788       798       808       818       828       838       848       858       868       878     
                                                                                                                                                                                                                                                                                                                                                                                                                                       404|                                  455|                                                                                                                                                                                                                                                                            741|                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                        418                                   470                                                                                                                                                                                                                                                                             747
   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 5JJR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5hmy 5hmz 5hn0 5i3p 5i3q 5iq6 5jjs

(-) Related Entries Specified in the PDB File

5jjs