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(-) Description

Title :  CRYSTAL STRUCTURE OF A HPIV HAEMAGGLUTININ-NEURAMINIDASE-INHIBITOR COMPLEX
 
Authors :  L. Dirr, I. M. El-Deeb, L. M. G. Chavas, P. Guillon, M. Von Itzstein
Date :  13 Jul 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Haemagglutinin-Neuraminidase, Hydrolase, Viral Protein, Host Cell Surface Receptor Binding, Hydrolase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Dirr, I. M. El-Deeb, L. M. G. Chavas, P. Guillon, M. V. Itzstein
The Impact Of The Butterfly Effect On Human Parainfluenza Virus Haemagglutinin-Neuraminidase Inhibitor Design.
Sci Rep V. 7 4507 2017
PubMed-ID: 28674426  |  Reference-DOI: 10.1038/S41598-017-04656-Y

(-) Compounds

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
    Atcc: VR-93
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9 CELLS
    Expression System Taxid: 7108
    Organism Scientific: HUMAN PARAINFLUENZA VIRUS 3
    Organism Taxid: 11216

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 24)

Asymmetric/Biological Unit (9, 24)
No.NameCountTypeFull Name
16Y62Ligand/Ion(2~{R},3~{R},4~{S})-4-[4-(METHOXYMETHYL)-1,2,3-TRIAZOL-1-YL]-3-(2-METHYLPROPANOYLAMINO)-2-[(1~{R},2~{R})-1,2,3-TRIS(OXIDANYL)PROPYL]-3,4-DIHYDRO-2~{H}-PYRAN-6-CARBOXYLIC ACID
2BMA2Ligand/IonBETA-D-MANNOSE
3CA2Ligand/IonCALCIUM ION
4CIT1Ligand/IonCITRIC ACID
5EDO6Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7MAN1Ligand/IonALPHA-D-MANNOSE
8NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
9SO41Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:351 , THR A:353 , TRP A:451 , NAG A:602binding site for residue NAG A 601
02AC2SOFTWARETRP A:451 , NAG A:601 , BMA A:604binding site for residue NAG A 602
03AC3SOFTWAREARG A:522 , ASN A:523 , HOH A:717 , HOH A:838 , HOH A:932binding site for residue NAG A 603
04AC4SOFTWARENAG A:602 , HOH A:707 , HOH A:975binding site for residue BMA A 604
05AC5SOFTWAREASP A:279 , SER A:282 , GLY A:284 , ALA A:316 , HOH A:735binding site for residue CA A 605
06AC6SOFTWAREARG A:192 , THR A:193 , ASN A:208 , ILE A:210 , LYS A:254 , GLU A:276 , TYR A:319 , TYR A:337 , GLU A:409 , ARG A:424 , ARG A:502 , TYR A:530 , HOH A:727 , HOH A:768 , HOH A:803 , HOH A:842 , HOH A:849 , HOH A:865 , HOH A:973binding site for residue 6Y6 A 606
07AC7SOFTWARETYR A:266 , GLY A:330 , LYS A:331 , ILE A:332 , VAL A:384binding site for residue EDO A 607
08AC8SOFTWAREASP A:497 , GLN A:499 , ARG A:515 , HOH A:733binding site for residue EDO A 608
09AC9SOFTWAREPHE A:247 , ASN A:248 , HOH A:763 , SER B:233binding site for residue EDO A 609
10AD1SOFTWARETHR A:302 , ARG A:303 , ASN A:308 , HOH A:723binding site for residue NAG A 610
11AD2SOFTWARESER A:244 , HIS A:245 , THR A:246 , HOH A:720 , HOH A:738 , HOH A:763 , HOH A:960 , THR B:230 , VAL B:231 , ASP B:238binding site for residue CIT A 611
12AD3SOFTWAREASN B:351 , TRP B:451 , NAG B:602 , HOH B:701binding site for residue NAG B 601
13AD4SOFTWARELYS A:273 , LYS A:305 , TRP B:451 , NAG B:601 , BMA B:604binding site for residue NAG B 602
14AD5SOFTWAREASN B:523 , THR B:525 , HOH B:702 , HOH B:772binding site for residue NAG B 603
15AD6SOFTWARENAG B:602 , MAN B:612binding site for residue BMA B 604
16AD7SOFTWAREASP B:279 , SER B:282 , GLY B:284 , ALA B:316 , HOH B:738binding site for residue CA B 605
17AD8SOFTWAREARG B:192 , THR B:193 , ASN B:208 , ILE B:210 , CYS B:214 , LYS B:254 , GLU B:276 , TYR B:319 , TYR B:337 , GLU B:409 , ARG B:424 , ARG B:502 , TYR B:530 , HOH B:767 , HOH B:881binding site for residue 6Y6 B 606
18AD9SOFTWARETRP B:465 , ASP B:497 , GLN B:499 , HOH B:915binding site for residue EDO B 607
19AE1SOFTWARETYR B:266 , GLY B:330 , LYS B:331 , ILE B:332 , VAL B:384binding site for residue EDO B 608
20AE2SOFTWAREASN A:460 , ASN A:461 , HOH A:964 , PRO B:356 , HOH B:778binding site for residue EDO B 609
21AE3SOFTWAREHIS A:552 , LYS A:553 , SER A:554 , HIS B:552 , LYS B:553 , SER B:554 , LEU B:555 , HOH B:707binding site for residue SO4 B 610
22AE4SOFTWARETHR B:302 , ARG B:303 , ASN B:308 , HOH B:820binding site for residue NAG B 611
23AE5SOFTWARETRP B:451 , THR B:513 , BMA B:604 , HOH B:842 , HOH B:844binding site for residue MAN B 612
24AE6SOFTWARETHR A:230 , VAL A:231 , ASN A:240 , SER B:244 , HIS B:245 , THR B:246 , HOH B:708 , HOH B:742binding site for residue GOL B 613

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:159 -A:571
2A:190 -A:214
3A:256 -A:269
4A:350 -A:363
5A:355 -A:469
6A:463 -A:473
7A:535 -A:544
8B:159 -B:571
9B:190 -B:214
10B:256 -B:269
11B:350 -B:363
12B:355 -B:469
13B:463 -B:473
14B:535 -B:544

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:169 -Pro A:170
2Thr B:169 -Pro B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KV8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KV8)

(-) Exons   (0, 0)

(no "Exon" information available for 5KV8)

(-) Sequences/Alignments

Asymmetric/Biological 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhh.....eeee.......................eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..eeeeeee....hhhhhhhh.....eeeeee.....eeeeeehhhhhee...eeeeee.....eee..eeeeeeeeee..................hhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeee...........eeeeee..eeeeee.........eeeeee.......eeee...............................eee.......eeeeee........eeeeee....eeeeee.......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee..eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kv8 A 143 THDVGIKPLNPDDFWRCTSGLPSLMKTPKIRLMPGPGLLAMPTTVDGCVRTPSLVINDLIYAYTSNLITRGCQDIGKSYQVLQIGIITVNSDLVPDLNPRISHTFNINDNRKSCSLALLNTDVYQLCSTPKVDERSDYASSGIEDIVLDIVNHDGSISTTRFKNNNISFDQPYAALYPSVGPGIYYKGKIIFLGYGGLEHPINENAICNTTGCPGKTQRDCNQASHSPWFSDRRMVNSIIVVDKGLNSIPKLKVWTISMRQNYWGSEGRLLLLGNKIYIYTRSTSWHSKLQLGIIDITDYSDIRIKWTWHNVLSRPGNNECPWGHSCPDGCITGVYTDAYPLNPTGSIVSSVILDSQKSRVNPVITYSTATERVNELAIRNKTLSAGYTTTSCITHYNKGYCFHIVEINHKSLDTFQPMLFKTEIPKSCS 572
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572


Chain B from PDB  Type:PROTEIN  Length:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.hhhhhh.....ee.......................eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..eeeeeee....hhhhhhhh.....eeeeee.....eeeeeehhhhhee...eeeeee.....eee..eeeeeeeeee..................hhhhhhhhhhhhhhh...eeeeeeeee...eeeeee...........eeeeee..eeeeee.........eeeeee.......eeee...............................eee......eeeeeee........eeeeeee...eeeeee.......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kv8 B 142 ITHDVGIKPLNPDDFWRCGLPSLMKTPKIRLMPGPGLLAMPTTVDGCVRTPSLVINDLIYAYTSNLITRGCQDIGKSYQVLQIGIITVNSDLVPDLNPRISHTFNINDNRKSCSLALLNTDVYQLCSTPKVDERSDYASSGIEDIVLDIVNHDGSISTTRFKNNNISFDQPYAALYPSVGPGIYYKGKIIFLGYGGLEHPINENAICNTTGCPGKTQRDCNQASHSPWFSDRRMVNSIIVVDSIPKLKVWTISMRQNYWGSEGRLLLLGNKIYIYTRSTSWHSKLQLGIIDITDYSDIRIKWTWHNVLSRPGNNECPWGHSCPDGCITGVYTDAYPLNPTGSIVSSVILDSQKSRVNPVITYSTATERVNELAIRNKTLSAGYTTTSCITHYNKGYCFHIVEINHKSLDTFQPMLFKTEIPKSC 571
                                   151       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 ||    397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567    
                                           159|                                                                                                                                                                                                                            385|                                                                                                                                                                                     
                                            162                                                                                                                                                                                                                             390
   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 5KV8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KV8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KV8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5KV8)

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  5kv8
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  3.2.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        G8G134_9MONO | G8G134: 5kv9
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        G8G134_9MONO | G8G134: 4xjq 4xjr

(-) Related Entries Specified in the PDB File

4xjq 4XJQ CONTAINS THE SAME PROTEIN AS APO FORM.
4xjr 4XJR CONTAINS THE SAME PROTEIN COMPLEXED WITH OEL.
5kv9