Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH SAH
 
Authors :  Y. Zhao, S. Soh, J. Zheng, W. W. Phoo, K. Swaminathan, T. C. Cornvik, S. P. P. -Y. Shi, J. Lescar, S. G. Vasudevan, D. Luo
Date :  18 Sep 14  (Deposition) - 28 Jan 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Methyltransferase, Rna-Dependent Rna Polymerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, T. S. Soh, J. Zheng, K. W. K. Chan, W. W. Phoo, C. C. Lee, M. Y. F. Tay, K. Swaminathan, T. C. Cornvik, S. P. Lim, P. Shi, J. Lescar, S. G. Vasudevan, D. Luo
A Crystal Structure Of The Dengue Virus Ns5 Protein Reveals A Novel Inter-Domain Interface Essential For Protein Flexibility And Virus Replication.
Plos Pathog. V. 11 04682 2015
PubMed-ID: 25775415  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004682

(-) Compounds

Molecule 1 - NS5 POLYMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: CODON PLUS
    Expression System Vector: PNIC28-BSA4
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2494-3385
    Organism Scientific: DENGUE VIRUS 3
    Organism Taxid: 11069
    Strain: SINGAPORE STRAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:437 , HIS A:441 , CYS A:446 , CYS A:449BINDING SITE FOR RESIDUE ZN A1001
02AC2SOFTWAREHIS A:712 , HIS A:714 , CYS A:728 , CYS A:847BINDING SITE FOR RESIDUE ZN A1002
03AC3SOFTWARESER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:86 , TRP A:87 , 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:2042 , HOH A:2044 , HOH A:2061BINDING SITE FOR RESIDUE SAH A1051
04AC4SOFTWAREARG A:57 , LYS A:61 , LEU A:209 , HOH A:2030BINDING SITE FOR RESIDUE ACT A1884
05AC5SOFTWAREARG A:38 , LYS A:42 , HOH A:2027BINDING SITE FOR RESIDUE ACT A1885
06AC6SOFTWARELYS A:14 , ASN A:18 , SER A:213BINDING SITE FOR RESIDUE ACT A1886
07AC7SOFTWAREHIS A:52BINDING SITE FOR RESIDUE ACT A1887
08AC8SOFTWAREGLU A:112 , SER A:522 , LYS A:668 , HIS A:701BINDING SITE FOR RESIDUE ACT A1888
09AC9SOFTWAREHOH A:2073BINDING SITE FOR RESIDUE ACT A1889
10BC1SOFTWAREASP A:256 , GLY A:258 , LYS A:300 , LYS A:355 , GLU A:356 , ASP A:359BINDING SITE FOR RESIDUE GOL A1890

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V0Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4V0Q)

(-) 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:851
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhh....eee.hhhhhhhhhh.........hhhhhhhhhhhh......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eee..........hhhhh....hhhhhhhhhhhhhhhh...............eeeeeee...........hhhhhh.hhhhh.hhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v0q A   6 GETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNWDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMSRAIWYMWLGVRYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM 883
                                    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       305       315       325       335       345       355       365       375       385       395       405|      427       437       447      |472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882 
                                                                                                                                                                                                                                                                                                                                                                                                                                         405|                                 454|                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                          418                                  470
   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 4V0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V0Q)

(-) Gene Ontology  (62, 107)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4v0q)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4v0q
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POLG_DEN3I | Q5UB51
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q6DLV0_9FLAV | Q6DLV0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  POLG_DEN3I | Q5UB51
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q6DLV0_9FLAV | Q6DLV0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_DEN3I | Q5UB51: 3u1i 3u1j 4ctj 4ctk 4v0r
        Q6DLV0_9FLAV | Q6DLV0: 3j6s 3j6t 3j6u
UniProtKB/TrEMBL
        Q6DLV0_9FLAV | Q6DLV0: 2j7u 2j7w 3vws 4c11 4hhj 4v0r 5dto 5eiw 5f3t 5f3z 5f41 5hmw 5hmx 5hmy 5hmz 5hn0 5i3p 5i3q 5iq6 5jjr 5jjs

(-) Related Entries Specified in the PDB File

4v0r DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH GTP AND SAH