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(-) Description

Title :  CRYSTAL STRUCTURE OF INHIBITOR JNJ-2408068 IN COMPLEX WITH PREFUSION RSV F GLYCOPROTEIN
 
Authors :  M. B. Battles, J. S. Mclellan, E. Arnoult, J. P. Langedijk, D. Roymans
Date :  15 Oct 15  (Deposition) - 09 Dec 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  F
Biol. Unit 1:  F  (3x)
Keywords :  Class I Viral Fusion Protein, Fusion, Respiratory Syncytial Virus, Prefusion, Viral Protein, Fusion Inhibitor, Cell Invasion-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Battles, J. P. Langedijk, P. Furmanova-Hollenstein, S. Chaiwatpongsakorn, H. M. Costello, L. Kwanten, L. Vranckx, P. Vink S. Jaensch, T. H. Jonckers, A. Koul, E. Arnoult, M. E. Peeples, D. Roymans, J. S. Mclellan
Molecular Mechanism Of Respiratory Syncytial Virus Fusion Inhibitors.
Nat. Chem. Biol. V. 12 87 2016
PubMed-ID: 26641933  |  Reference-DOI: 10.1038/NCHEMBIO.1982

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 FREESTYLE
    Expression System Common: HUMAN
    Expression System Plasmid: P(ALPHA)H
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: RSV F ECTODOMAIN (UNP RESIDUES 1-513)
    Mutation: YES
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS A (STRAIN A2)
    Organism Taxid: 11259
    Strain: A2
    Synonym: PROTEIN F

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : F
Biological Unit 1 (3x): F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
15NK1Ligand/Ion2-[[2-[[1-(2-AZANYLETHYL)PIPERIDIN-4-YL]AMINO]-4-METHYL-BENZIMIDAZOL-1-YL]METHYL]-6-METHYL-PYRIDIN-3-OL
2NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
15NK3Ligand/Ion2-[[2-[[1-(2-AZANYLETHYL)PIPERIDIN-4-YL]AMINO]-4-METHYL-BENZIMIDAZOL-1-YL]METHYL]-6-METHYL-PYRIDIN-3-OL
2NHE3Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
3SO418Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE F:387 , PHE F:477 , TYR F:478 , ASP F:479 , ASN F:496 , ILE F:499 , LEU F:503binding site for residue NHE F 601
2AC2SOFTWAREASN F:276 , ASN F:277 , ARG F:364binding site for residue SO4 F 602
3AC3SOFTWAREPHE F:137 , ARG F:339 , HOH F:726binding site for residue SO4 F 603
4AC4SOFTWARESER F:443 , LYS F:445 , SER F:466 , HOH F:706binding site for residue SO4 F 604
5AC5SOFTWAREVAL F:239 , ASN F:240binding site for residue SO4 F 605
6AC6SOFTWAREASN F:444 , GLY F:446 , LYS F:461binding site for residue SO4 F 606
7AC7SOFTWARELYS F:156 , GLN F:462 , GLU F:463binding site for residue SO4 F 607
8AC8SOFTWAREPHE F:140 , MET F:396 , ASP F:486 , GLU F:487 , PHE F:488 , ASP F:489binding site for residue 5NK F 608

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1F:37 -F:439
2F:155 -F:290
3F:313 -F:343
4F:322 -F:333
5F:358 -F:367
6F:382 -F:393
7F:416 -F:422

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr F:245 -Pro F:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EA3)

(-) Exons   (0, 0)

(no "Exon" information available for 5EA3)

(-) 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 F from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeeeeeee.eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhh....eeeeee...eeeeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...ee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeee..eeeeeeeeeee..ee..........eeee...eeeeee..eeeee.hhhhheee..eeeee.hhheeehhhhhhhhhh........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee......eeeee...hhhhhhhhhhh...eeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ea3 F  27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKKVKLIKQELDKYKNAVTELQLLMFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFI 506
                                    36        46        56        75        85        95 ||    144       154       164       174       184       194       204|      227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497         
                                                                 65|                    97|                                                                204|                                                                                                                                                                                                                                                                                                
                                                                  75                    137                                                                 218
   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 5EA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EA3)

(-) Gene Ontology  (12, 12)

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    Thr F:245 - Pro F:246   [ RasMol ]  
 
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  FUS_HRSVA | P03420
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUS_HRSVA | P03420: 2mdp 3ixt 3kpe 3o41 3o45 3rki 3rrr 3rrt 4ccf 4jhw 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4zyp 5c69 5c6b 5ea4 5ea5 5ea6 5ea7 5ea8 5j3d 5k6b 5k6c 5k6f 5k6g 5k6h 5k6i 5toj 5tok 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

4mmu PREFUSION-STABILIZED RSV F GLYCOPROTEIN WITHOUT BOUND INHIBITOR
5ea4
5ea5
5ea6
5ea7
5ea8