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(-) Description

Title :  DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND COMPOUND BF175
 
Authors :  K. Barral, G. Bricogne, A. Sharff
Date :  20 Oct 15  (Deposition) - 26 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Fragment-Based Drug Design Dengue Virus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Benmansour, I. Trist, B. Coutard, E. Decroly, G. Querat, A. Brancale, K. Barral
Discovery Of Novel Dengue Virus Ns5 Methyltransferase Non-Nucleoside Inhibitors By Fragment-Based Drug Design.
Eur. J. Med. Chem. V. 125 865 2016
PubMed-ID: 27750202  |  Reference-DOI: 10.1016/J.EJMECH.2016.10.007

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A, C
    EC Number: 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLASMID
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Organism Common: DENV-3
    Organism Scientific: DENGUE VIRUS TYPE 3 (STRAIN PHILIPPINES/H87/1956)
    Organism Taxid: 408870
    Strain: PHILIPPINES/H87/1956

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
15LP1Ligand/Ion2-[(2-AZANYL-4-CHLORANYL-PHENYL)CARBAMOYLAMINO]-4-METHYL-BENZOIC ACID
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
15LP1Ligand/Ion2-[(2-AZANYL-4-CHLORANYL-PHENYL)CARBAMOYLAMINO]-4-METHYL-BENZOIC ACID
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15LP-1Ligand/Ion2-[(2-AZANYL-4-CHLORANYL-PHENYL)CARBAMOYLAMINO]-4-METHYL-BENZOIC ACID
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER 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:410 , HOH A:413 , HOH A:423 , HOH A:588binding site for residue SAM A 301
2AC2SOFTWAREARG A:84 , GLY A:107 , PRO A:108 , GLY A:109 , HIS A:110 , GLU A:112 , MET A:233 , HOH A:451 , HOH A:507 , HOH A:551binding site for residue 5LP A 302
3AC3SOFTWARESER C:56 , GLY C:58 , GLY C:81 , CYS C:82 , GLY C:83 , GLY C:86 , TRP C:87 , THR C:104 , LYS C:105 , HIS C:110 , LYS C:130 , ASP C:131 , VAL C:132 , PHE C:133 , ASP C:146 , ILE C:147 , HOH C:4102 , HOH C:4124 , HOH C:4169 , HOH C:4229binding site for residue SAM C 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EC8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EC8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EC8)

(-) Exons   (0, 0)

(no "Exon" information available for 5EC8)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh.........hhhhhhhhhhhh......eeeeee....hhhhhhhhh...eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhh........eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ec8 A   7 ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTR 262
                                    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      


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhh.........hhhhhhhhhhh.......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ec8 C   7 ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTR 262
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 5EC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EC8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EC8)

(-) Gene Ontology  (62, 62)

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_DEN3P | P27915: 1uzg 2j7u 2j7w 3p8z 3p97 3uze 3vtt 5ccv 5e9q 5ehg 5ehi 5eif 5eiw 5ekx

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