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(-) Description

Title :  INFLUENZA HEMAGGLUTININ H3 A/HONG KONG/1/1968 IN COMPLEX WITH DESIGNED INHIBITOR PROTEIN HSB.2A
 
Authors :  S. M. Bernard, I. A. Wilson
Date :  13 Jul 16  (Deposition) - 14 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I
Keywords :  Influenza, Inhibitor, Complex, Design, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Strauch, S. M. Bernard, D. La, A. J. Bohn, P. S. Lee, C. E. Anderson, T. Nieusma, C. A. Holstein, N. K. Garcia, K. A. Hooper, R. Ravichandran J. W. Nelson, W. Sheffler, J. D. Bloom, K. K. Lee, A. B. Ward, P. Yager, D. H. Fuller, I. A. Wilson, D. Baker
Computational Design Of Trimeric Influenza-Neutralizing Proteins Targeting The Hemagglutinin Receptor Binding Site.
Nat. Biotechnol. 2017
PubMed-ID: 28604661  |  Reference-DOI: 10.1038/NBT.3907

(-) 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
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/HONG KONG/1/1968 H3N2)
    Organism Taxid: 506350
    Strain: A/HONG KONG/1/1968 H3N2
 
Molecule 3 - DESIGNED INFLUENZA INHIBITOR HSB.2A
    Chains: G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:38 , ALA A:39binding site for Mono-Saccharide NAG A 402 bound to ASN A 38
02AC2SOFTWAREASN A:165 , THR A:167 , HOH A:588 , SER C:219 , TRP C:222binding site for Poly-Saccharide residues NAG A 403 through NAG A 404 bound to ASN A 165
03AC3SOFTWAREASN A:285 , VAL A:297 , HOH A:510 , HOH A:549binding site for Mono-Saccharide NAG A 401 bound to ASN A 285
04AC4SOFTWAREGLU B:479 , ASN B:483 , THR B:485binding site for Mono-Saccharide NAG B 601 bound to ASN B 483
05AC5SOFTWAREASN C:38 , THR C:318 , LEU D:381binding site for Poly-Saccharide residues NAG C 403 through NAG C 404 bound to ASN C 38
06AC6SOFTWAREASN C:165 , THR C:167 , SER E:219 , PRO E:221 , TRP E:222binding site for Poly-Saccharide residues NAG C 401 through NAG C 402 bound to ASN C 165
07AC7SOFTWAREASN C:285 , GLU D:398binding site for Poly-Saccharide residues NAG C 405 through NAG C 406 bound to ASN C 285
08AC8SOFTWAREALA D:476 , GLU D:479 , ASN D:483 , HOH D:709binding site for Mono-Saccharide NAG D 601 bound to ASN D 483
09AC9SOFTWAREASN E:38 , ALA E:39 , HOH E:552binding site for Mono-Saccharide NAG E 405 bound to ASN E 38
10AD1SOFTWARESER A:219 , PRO A:221 , TRP A:222 , ASN E:165 , THR E:167binding site for Poly-Saccharide residues NAG E 402 through BMA E 404 bound to ASN E 165
11AD2SOFTWAREASN E:285 , HOH F:702binding site for Mono-Saccharide NAG E 401 bound to ASN E 285
12AD3SOFTWAREALA F:476 , GLU F:479 , ASN F:483binding site for Poly-Saccharide residues NAG F 601 through NAG F 602 bound to ASN F 483

(-) SS Bonds  (20, 20)

Asymmetric/Biological Unit
No.Residues
1A:14 -B:466
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:473 -B:477
7C:14 -D:466
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:473 -D:477
13E:14 -F:466
14E:52 -E:277
15E:64 -E:76
16E:97 -E:139
17E:281 -E:305
18F:473 -F:477
19G:11 -G:43
20H:11 -H:43

(-) 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 5KUY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KUY)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               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...................eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhhh....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
                 5kuy A   7 ADPGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPE 325
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kuy B 330 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGV 505
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499      


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               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.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....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
                 5kuy C   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVP 324
                                    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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kuy D 330 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQ 501
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499  


Chain E 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..hhhhhhhhhh....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
                 5kuy E   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 F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kuy F 330 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 500
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499 


Chain G from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeee.....eeeeeeeeeeehhhheeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 5kuy G   5 IVNVPNCNTTKYQQLARTAVAIYNYHEQAHLTFVENLNCKEQGNYYYITLAATDDAGKKAIYEAKIGVVESAGWTGVEEFKLVG  88
                                    14        24        34        44        54        64        74        84    


Chain H from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeee.....eeeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5kuy H   5 IVNVPNCNTTKYQQLARTAVAIYNYHEQAHLTFVENLNCKEQGNYYYITLAATDDAGKKAIYEAKIGVVESAGWTGVEEFKLVGS  89
                                    14        24        34        44        54        64        74        84     


Chain I from PDB  Type:PROTEIN  Length:53
                                                                                     
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.........ee.......eeee....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 5kuy I  11 CNTKYQQLARTAVAIYNYHEQAHLTFVENYYYITLAAKIGVVESAGWTGVEEF  84
                              ||    21        31       |49      ||71        81   
                             13|                      39|      56|               
                              15                       48       69
   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 5KUY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kuy
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  HEMA_I68A4 | Q91MA7
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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 5t6n 5thf 5umn 5vtq 5vtr 5vtu 5vtv 5vtw 5vtx 5vty 5vtz 5vu4

(-) Related Entries Specified in the PDB File

5kux