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(-) Description

Title :  STRUCTURE OF A/HUBEI/1/2010 H5 HA
 
Authors :  D. A. Shore, H. Yang, P. J. Carney, J. C. Chang, J. Stevens
Date :  20 May 13  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  B,D,F  (1x)
Biol. Unit 2:  A,C,E  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Hemagglutinin, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Shore, H. Yang, A. L. Balish, S. S. Shepard, P. J. Carney, J. C. Chang, C. T. Davis, R. O. Donis, J. M. Villanueva, A. I. Klimov, J. Stevens
Structural And Antigenic Variation Among Diverse Clade 2 H5N1 Viruses.
Plos One V. 8 75209 2013
PubMed-ID: 24086467  |  Reference-DOI: 10.1371/JOURNAL.PONE.0075209

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A, E, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: HA1 RESIDUES 17-342
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1087279
    Strain: A/HUBEI/1/2010(H5N1)
 
Molecule 2 - HEMAGGLUTININ
    Chains: B, F, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: HA2 RESIDUES 346-523
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1087279
    Strain: A/HUBEI/1/2010(H5N1)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):  B D F
Biological Unit 2 (1x): A C E 
Biological Unit 3 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 11)
No.NameCountTypeFull Name
1NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:11BINDING SITE FOR MONO-SACCHARIDE NAG A 406 BOUND TO ASN A 11
02AC2SOFTWAREASN A:23BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 23 RESIDUES 404 TO 405
03AC3SOFTWAREASN A:165 , ASN A:236 , ASP A:237 , ALA A:238 , SER E:217BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 165 RESIDUES 402 TO 403
04AC4SOFTWAREARG A:277 , ASN A:286BINDING SITE FOR MONO-SACCHARIDE NAG A 401 BOUND TO ASN A 286
05AC5SOFTWAREGLU B:147 , ASN B:154BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 154 RESIDUES 201 TO 202
06AC6SOFTWAREASN C:11BINDING SITE FOR MONO-SACCHARIDE NAG C 403 BOUND TO ASN C 11
07AC7SOFTWAREASN C:23BINDING SITE FOR MONO-SACCHARIDE NAG C 402 BOUND TO ASN C 23
08AC8SOFTWARESER A:217 , ASN C:165 , ASN C:236 , ASP C:237 , ALA C:238BINDING SITE FOR MONO-SACCHARIDE NAG C 401 BOUND TO ASN C 165
09AC9SOFTWAREASN E:23BINDING SITE FOR MONO-SACCHARIDE NAG E 402 BOUND TO ASN E 23
10BC1SOFTWARESER C:217 , ASN E:165 , ASN E:236 , ASP E:237 , ALA E:238BINDING SITE FOR MONO-SACCHARIDE NAG E 401 BOUND TO ASN E 165
11BC2SOFTWAREGLN E:169 , LYS E:255 , GLU F:147 , GLU F:150 , SER F:151 , ASN F:154BINDING SITE FOR MONO-SACCHARIDE NAG F 201 BOUND TO ASN F 154

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:4 -B:137
2A:42 -A:274
3A:55 -A:67
4A:90 -A:135
5A:278 -A:302
6B:144 -B:148
7C:4 -D:137
8C:42 -C:274
9C:55 -C:67
10C:90 -C:135
11C:278 -C:302
12D:144 -D:148
13E:4 -F:137
14E:42 -E:274
15E:55 -E:67
16E:90 -E:135
17E:278 -E:302
18F:144 -F:148

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:69 -Phe A:70
2Ile A:71 -Asn A:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KTH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KTH)

(-) Exons   (0, 0)

(no "Exon" information available for 4KTH)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ktha_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh...............eee...............hhhhhhhhhh...eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee......eee....eeeeee.eee..ee......ee......eee..ee......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth A   0 GDHICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPANDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKNSWSDHEASLGVSAACPYQGKSSFFRNVVWLIKKDNAYPTIKKGYNNTNQEDLLVLWGIHHPNDEAEQTRLYQNPTTYISIGTSTLNQRLVPKIATRSKINGQSGRIDFFWTILKPNDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSEVEYGNCNTRCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSP 321
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319  


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains d4kthb_ B: Influenza hemagglutinin (stalk)                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth B  10 IEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVRNLYDKVRLQLKDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEIS 174
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     


Chain C from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kthc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh...............eee...............hhhhhhhhh....eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee......eee....eeeeee.eee..ee......ee......eee..ee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth C   0 GDHICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPANDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKNSWSDHEASLGVSAACPYQGKSSFFRNVVWLIKKDNAYPTIKKGYNNTNQEDLLVLWGIHHPNDEAEQTRLYQNPTTYISIGTSTLNQRLVPKIATRSKINGQSGRIDFFWTILKPNDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSEVEYGNCNTRCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNS 320
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319 


Chain D from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4kthd_ D: Influenza hemagglutinin (stalk)                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.........eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth D   6 IAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVRNLYDKVRLQLKDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISS 175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175


Chain E from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kthe_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh...............eee...............hhhhhhhhh....eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee......eee....eeeeee.eee..ee......ee......eee..ee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth E   0 GDHICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPANDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKNSWSDHEASLGVSAACPYQGKSSFFRNVVWLIKKDNAYPTIKKGYNNTNQEDLLVLWGIHHPNDEAEQTRLYQNPTTYISIGTSTLNQRLVPKIATRSKINGQSGRIDFFWTILKPNDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSEVEYGNCNTRCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNS 320
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319 


Chain F from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains d4kthf_ F: Influenza hemagglutinin (stalk)                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kth F  10 IEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVRNLYDKVRLQLKDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREE 172
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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  (2, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KTH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KTH)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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4kw1 4kwm