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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A/HONG KONG/1/1968 (H3N2) INFLUENZA VIRUS HEMAGGLUTININ IN COMPLEX WITH THE ANTIVIRAL DRUG ARBIDOL
 
Authors :  R. U. Kadam, I. A. Wilson
Date :  01 Sep 16  (Deposition) - 04 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Viral Protein, Ectodomain, N-Glycosylation, Antiviral (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. U. Kadam, I. A. Wilson
Structural Basis Of Influenza Virus Fusion Inhibition By Th Antiviral Drug Arbidol.
Proc. Natl. Acad. Sci. V. 114 206 2017 U. S. A.
PubMed-ID: 28003465  |  Reference-DOI: 10.1073/PNAS.1617020114

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A, C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/HONG KONG/1/1968 H3N2)
    Organism Taxid: 506350
    Strain: A/HONG KONG/1/1968 H3N2
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B, D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HA
    Organism Common: INFLUENZA A VIRUS (STRAIN NT60)
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/NORTHERN TERRITORY/60/1968 H3N2)
    Organism Taxid: 384505
    Strain: A/NORTHERN TERRITORY/60/1968 H3N2

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 40)

Asymmetric/Biological Unit (6, 40)
No.NameCountTypeFull Name
175U3Ligand/IonETHYL 6-BROMO-4-[(DIMETHYLAMINO)METHYL]-5-HYDROXY-1-METHYL-2-[(PHENYLSULFANYL)METHYL]-1H-INDOLE-3-CARBOXYLATE
2BMA3Ligand/IonBETA-D-MANNOSE
3GOL2Ligand/IonGLYCEROL
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG25Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:310 , GLN A:311 , TYR B:94 , GLU B:97 , HOH B:325 , PHE E:294 , LYS E:307 , ARG F:54 , VAL F:55 , GLU F:57 , LYS F:58binding site for residue 75U B 201
02AC2SOFTWARELYS B:139 , ARG F:127 , HIS F:159 , ASP F:160binding site for residue SO4 B 203
03AC3SOFTWAREARG B:127 , HIS B:159 , ASP B:160 , LYS D:139binding site for residue SO4 B 204
04AC4SOFTWAREARG A:208 , HOH A:544 , SER C:95 , ARG C:224 , HOH C:569binding site for residue SO4 C 410
05AC5SOFTWARELYS C:92 , ASP C:271 , PRO C:273 , HOH C:506binding site for residue GOL C 411
06AC6SOFTWAREPHE A:294 , LYS A:307 , ARG B:54 , GLU B:57 , LYS C:310 , GLN C:311 , ASP D:90 , SER D:93 , TYR D:94 , GLU D:97 , ALA D:101binding site for residue 75U D 201
07AC7SOFTWAREPHE C:294 , ARG D:54 , VAL D:55 , GLU D:57 , LYS D:58 , THR D:59 , LYS E:310 , GLN E:311 , SER F:93 , TYR F:94 , GLU F:97binding site for residue 75U D 202
08AC8SOFTWAREARG D:127 , HIS D:159 , ASP D:160 , LYS F:139binding site for residue SO4 D 205
09AC9SOFTWAREARG E:90 , LYS E:92 , ASP E:271 , PRO E:273 , HOH E:506 , HOH E:522 , HOH E:554binding site for residue GOL E 410
10AD1SOFTWAREASN A:22 , GLU A:35binding site for Mono-Saccharide NAG A 401 bound to ASN A 22
11AD2SOFTWAREASN A:38 , THR A:318binding site for Mono-Saccharide NAG A 402 bound to ASN A 38
12AD3SOFTWAREASN A:81 , GLU A:119binding site for Mono-Saccharide NAG A 403 bound to ASN A 81
13AD4SOFTWAREASN A:165 , THR A:167 , SER C:219binding site for Poly-Saccharide residues NAG A 404 through MAN A 407 bound to ASN A 165
14AD5SOFTWARESER A:45 , ASN A:285 , VAL A:297 , HOH A:536 , GLU B:69binding site for Poly-Saccharide residues NAG A 408 through NAG A 409 bound to ASN A 285
15AD6SOFTWAREALA B:147 , GLU B:150 , ASN B:154binding site for Mono-Saccharide NAG B 202 bound to ASN B 154
16AD7SOFTWAREASN C:38 , THR C:318 , GLY D:31 , LEU D:52binding site for Poly-Saccharide residues NAG C 401 through NAG C 402 bound to ASN C 38
17AD8SOFTWAREPRO A:324 , LYS A:326 , ASN C:81 , GLU C:119 , PHE C:120 , ILE C:121 , TYR C:257binding site for Poly-Saccharide residues NAG C 403 through NAG C 404 bound to ASN C 81
18AD9SOFTWAREASN C:165 , THR C:167 , SER E:219 , PRO E:221 , TRP E:222binding site for Poly-Saccharide residues NAG C 405 through BMA C 407 bound to ASN C 165
19AE1SOFTWAREASN C:285 , HOH C:546binding site for Poly-Saccharide residues NAG C 408 through NAG C 409 bound to ASN C 285
20AE2SOFTWAREALA D:147 , GLU D:150 , ASN D:154 , THR D:156binding site for Poly-Saccharide residues NAG D 203 through NAG D 204 bound to ASN D 154
21AE3SOFTWAREPRO A:143 , ASN E:38 , THR E:318binding site for Mono-Saccharide NAG E 401 bound to ASN E 38
22AE4SOFTWAREGLN E:80 , ASN E:81 , GLU E:119 , PHE E:120 , ILE E:121 , HOH E:577binding site for Mono-Saccharide NAG E 402 bound to ASN E 81
23AE5SOFTWARESER A:219 , PRO A:221 , TRP A:222 , HOH A:501 , ASN E:165 , THR E:167 , HOH E:543binding site for Poly-Saccharide residues NAG E 403 through MAN E 407 bound to ASN E 165
24AE6SOFTWAREASN E:285 , VAL E:297 , GLU F:69binding site for Poly-Saccharide residues NAG E 408 through NAG E 409 bound to ASN E 285
25AE7SOFTWAREALA F:147 , GLU F:150 , ASN F:154binding site for Mono-Saccharide NAG F 201 bound to ASN F 154

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7C:14 -D:137
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:144 -D:148
13E:14 -F:137
14E:52 -E:277
15E:64 -E:76
16E:97 -E:139
17E:281 -E:305
18F:144 -F:148

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:54 -Pro A:55
2Asn C:54 -Pro C:55
3Asn E:54 -Pro E:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T6N)

(-) Exons   (0, 0)

(no "Exon" information available for 5T6N)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhh.....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee......eee..ee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t6n A   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK 326
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318        


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6n B   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhh.....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6n C   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPE 325
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6n D   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain E from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee......eee.......eee..eee.ee......eeee...eeee...hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhh.....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee...........ee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t6n E   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK 326
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318        


Chain F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6n F   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 5T6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T6N)

(-) Gene Ontology  (17, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5t6n
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  HEMA_I68A6 | P03436
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_I68A4 | Q91MA7: 3sdy 3ztj 4fnk 4fp8 4fqr 4fqy 4nm8 4ubd 4we4 4zcj 5k9k 5k9q 5kan 5kuy 5thf 5umn 5vtq 5vtr 5vtu 5vtv 5vtw 5vtx 5vty 5vtz 5vu4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T6N)