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 :  CRYSTAL STRUCTURE OF HUMAN ENTEROVIRUS D68
 
Authors :  Y. Liu, J. Sheng, A. Fokine, G. Meng, F. Long, R. J. Kuhn, M. G. Rossmann
Date :  08 Oct 14  (Deposition) - 14 Jan 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Enterovirus, Capsid, Beta Jelly Roll, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, J. Sheng, A. Fokine, G. Meng, W. H. Shin, F. Long, R. J. Kuhn, D. Kihara, M. G. Rossmann
Virus Structure. Structure And Inhibition Of Ev-D68, A Viru That Causes Respiratory Illness In Children.
Science V. 347 71 2015
PubMed-ID: 25554786  |  Reference-DOI: 10.1126/SCIENCE.1261962

(-) Compounds

Molecule 1 - VP1
    Chains: A
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
    Strain: FERMON CA62-1
 
Molecule 2 - VP2
    Chains: B
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
    Strain: FERMON CA62-1
 
Molecule 3 - VP3
    Chains: C
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
    Strain: FERMON CA62-1
 
Molecule 4 - VP4
    Chains: D
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
    Strain: FERMON CA62-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1DKA1Ligand/IonDECANOIC ACID
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1DKA60Ligand/IonDECANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:95 , THR A:97 , ILE A:119 , SER A:194 , MET A:241binding site for residue DKA A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WM8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:273 -Pro A:274
2Leu B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WM8)

(-) Exons   (0, 0)

(no "Exon" information available for 4WM8)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....................eehhhhh.....hhhhhh..........hhhhhhhhhhh..eeeeeeeeee......eeeee.....hhhhhhhhh.eeeeeeeeeeeeeeeeee......eeeeeeee..........hhhhhh...eeeeee.....eeeee........ee.................hhhhh.eeeeeee........eeeeeeeeeeeeeeeeeee............................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wm8 A   1 VESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLGRAALVSKKSFEYKNHHKNFFKWTINTKSFVQLRRKLELFTYLRFDAEITILTTVAVNGLPDLTLQAMFVPTGALTPKEQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTMPYMSIANANYKGRDTAPNTLNAIIGNRASVTTMPHNIVT 296
                                    10        20        30        40        50        60        70        87        97       107       117       127||     145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
                                                                                                         79|                                      128|                                                                                                                                                               
                                                                                                          87                                       137                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeee......ee.hhh..................hhhhh...ee...ee.......eeeeehhhhh.hhhhhhhhhheeeeeeeeeeeee.......eeeeeeeeee.............hhhhhhhhhhhee..hhhhh.......hhhhh.eeeee.....eeeeee................eeeeeeeeeeee........eeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wm8 B  10 SDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETSTDRFYTLRSVKWESNSTGWWWKLPDALNNIGMFGQNVQYHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHDTTTSPGFNDIMKGERGGTFNHPYVLDDGTSIACATIFPHQWINLRTNNSATIVLPWMNVAPMDFPLRHNQWTLAVIPVVPLGTRTMSSVVPITVSIAPMCCEFNGLRHAIT 247
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        


Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee.hhhhh....ee.........hhhhhhheeee.......eeeeee...........hhhhhhhh.eeeee..eeeeeee........eeeeeee........hhhhhh..eeeeee.....eeeeee........ee.............eeeeee............eeeeeeeeee....eeeee..............hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wm8 C   1 GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQIRNMLEMIQVESMMEINNTDGANGMERLRVDISVQADLDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSITLIIPWISGSHYRMFNSDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQSNHLHGAEAAYQ 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain D from PDB  Type:PROTEIN  Length:39
                                                                       
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......ee.hhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 4wm8 D  29 INFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVL  67
                                    38        48        58
   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 4WM8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WM8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WM8)

(-) Gene Ontology  (36, 41)

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
    DKA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:273 - Pro A:274   [ RasMol ]  
    Leu B:82 - Pro B:83   [ RasMol ]  
 
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
  4wm8
    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
  Q68T42_9ENTO | Q68T42
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q8QWD4_9ENTO | Q8QWD4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9YLJ3_9ENTO | Q9YLJ3
    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
  Q68T42_9ENTO | Q68T42
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8QWD4_9ENTO | Q8QWD4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9YLJ3_9ENTO | Q9YLJ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q68T42_9ENTO | Q68T42: 4wm7 5bnn 5bno 5bnp
        Q8QWD4_9ENTO | Q8QWD4: 4wm7
        Q9YLJ3_9ENTO | Q9YLJ3: 4wm7

(-) Related Entries Specified in the PDB File

4wm7