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(-) Description

Title :  CRYSTAL STRUCTURE OF EBOLA GLYCOPROTEIN IN COMPLEX WITH IBUPROFEN
 
Authors :  Y. Zhao, J. Ren, D. I. Stuart
Date :  04 May 16  (Deposition) - 29 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Ebola Virus, Filoviridae, Envelope Glycoprotein, Protein Inhibitor Complex, Ibuprofen, Toremifene, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, J. Ren, K. Harlos, D. M. Jones, A. Zeltina, T. A. Bowden, S. Padilla-Parra, E. E. Fry, D. I. Stuart
Toremifene Interacts With And Destabilizes The Ebola Virus Glycoprotein.
Nature V. 535 168 2016
PubMed-ID: 27362232  |  Reference-DOI: 10.1038/NATURE18615

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN 1,ENVELOPE GLYCOPROTEIN 1,ENVELOPE GLYCOPROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GP
    Mutation: YES
    Organism Scientific: EBOLA VIRUS - MAYINGA, ZAIRE, 1976
    Organism Taxid: 128952
    Synonym: GP1,2,GP,GP1,2,GP,GP1,2,GP
 
Molecule 2 - ENVELOPE GLYCOPROTEIN 2
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GP
    Organism Scientific: EBOLA VIRUS - MAYINGA, ZAIRE, 1976
    Organism Taxid: 128952
    Synonym: GP1,2,GP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL5Ligand/IonGLYCEROL
3IBP1Ligand/IonIBUPROFEN
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
5UNK7Mod. Amino Acid
Biological Unit 1 (4, 39)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2GOL15Ligand/IonGLYCEROL
3IBP3Ligand/IonIBUPROFEN
4NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
5UNK-1Mod. Amino Acid

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:69 , LEU A:70 , GLU A:71 , THR A:77 , ARG A:85 , ASN A:107 , TYR A:109 , GLU A:178binding site for residue GOL A 605
02AC2SOFTWAREPHE A:132 , VAL A:138 , THR A:175 , TYR A:213binding site for residue GOL A 606
03AC3SOFTWAREGLU A:120 , ASP A:150 , HOH A:707binding site for residue GOL A 607
04AC4SOFTWAREASN B:563 , GLU B:564 , GLN B:567 , NAG B:703binding site for residue GOL B 701
05AC5SOFTWAREASN B:512binding site for residue GOL B 702
06AC6SOFTWAREARG A:64 , ALA A:101 , LEU A:184 , TYR B:517 , MET B:548binding site for residue IBP B 706
07AC7SOFTWAREASN A:228 , GLU A:229binding site for Mono-Saccharide NAG A 602 bound to ASN A 228
08AC8SOFTWAREASN A:238 , LEU A:239binding site for Mono-Saccharide NAG A 603 bound to ASN A 238
09AC9SOFTWARETHR A:217 , LEU A:254 , ASN A:257 , GLU A:258 , TYR A:261 , ASN A:268 , THR A:269 , THR A:270binding site for Mono-Saccharide NAG A 601 bound to ASN A 257
10AD1SOFTWARETHR A:262 , GLY A:264 , LYS A:265 , ASN A:268binding site for Mono-Saccharide NAG A 604 bound to ASN A 268
11AD2SOFTWAREGLU A:156 , GLN B:508 , PRO B:509 , ASN B:563 , THR B:566 , GOL B:701 , HOH B:810 , HOH B:812 , HOH B:818binding site for Poly-Saccharide residues NAG B 703 through BMA B 705 bound to ASN B 563

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:53 -B:609
2A:108 -A:135
3A:121 -A:147
4B:511 -B:556
5B:601 -B:608

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JQB)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeee............hhh.eeeeeee.hhhh...hhhhhhh.eeee......eee..eee.eeeeeeeeee....................eeeeeeeeee......eeee....eee...eee.........eeeeeeeee..............eeeeeeee.......eeeeeee..eeee.....hhhhhhhhhhhhhhhh........eeeee................eee...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jqb A  32 SIPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTEWAFWETLSFTVVxxxxxxx 477
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  ||   217       227       237       247       257       267       277      |289   ||  310|||||||
                                                                                                                                                                                            194|                                                                      284|   293|  310|||||||
                                                                                                                                                                                             211                                                                       287    305   471-UNK||
                                                                                                                                                                                                                                                                                     472-UNK|
                                                                                                                                                                                                                                                                                      473-UNK
                                                                                                                                                                                                                                                                                       474-UNK
                                                                                                                                                                                                                                                                                        475-UNK
                                                                                                                                                                                                                                                                                         476-UNK
                                                                                                                                                                                                                                                                                          477-UNK


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.................hhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jqb B 502 EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD 632
                                   511       521       531       541       551       561       571       581       591       601       611       621       631
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5JQB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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        VGP_EBOZM | Q05320: 2ebo 2rlj 3csy 5fhc 5hj3 5jq3 5jq7 5kel 5kem 5ken

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