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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEMAGGLUTININ OF A/XINJIANG/1/2006 VIRUS
 
Authors :  X. Lu, Y. Shi, W. Zhang, Y. Zhang, J. Qi, G. F. Gao
Date :  25 Apr 13  (Deposition) - 24 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Homotrimer, Virus Attachment And Membrane Fusion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Lu, Y. Shi, W. Zhang, Y. Zhang, J. Qi, G. F. Gao
Structure And Receptor-Binding Properties Of An Airborne Transmissible Avian Influenza A Virus Hemagglutinin H5 (Vn1203Mut).
Protein Cell V. 4 502 2013
PubMed-ID: 23794001  |  Reference-DOI: 10.1007/S13238-013-3906-Z

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A, C, E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: RESIDUES 17-336
    Gene: HA
    Organism Common: A/XINJIANG/1/2006(H5N1)
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 577543
    Strain: (A/XINJIANG/1/2006(H5N1))
 
Molecule 2 - HEMAGGLUTININ
    Chains: B, D, F
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: RESIDUES 347-510
    Gene: HA
    Organism Common: A/CHICKEN/GUANGDONG/174/04(H5N1)
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 279728
    Strain: (A/CHICKEN/GUANGDONG/174/04(H5N1))

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:24BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWAREASN A:166 , ASN A:237 , ASP A:238 , HOH A:615BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREASN C:24BINDING SITE FOR RESIDUE NAG C 501
4AC4SOFTWAREASN C:166 , ASN C:237 , HOH C:613BINDING SITE FOR RESIDUE NAG C 502
5AC5SOFTWAREASN E:24BINDING SITE FOR RESIDUE NAG E 501
6AC6SOFTWAREASN E:166 , ASN E:237 , HOH E:607 , HOH E:613BINDING SITE FOR RESIDUE NAG E 502
7AC7SOFTWAREASN E:155BINDING SITE FOR RESIDUE NAG E 503

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:5 -B:137
2A:43 -A:275
3A:56 -A:68
4A:91 -A:136
5A:279 -A:303
6B:144 -B:148
7C:5 -D:137
8C:43 -C:275
9C:56 -C:68
10C:91 -C:136
11C:279 -C:303
12D:144 -D:148
13E:5 -F:137
14E:43 -E:275
15E:56 -E:68
16E:91 -E:136
17E:279 -E:303
18F:144 -F:148

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KDQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KDQ)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kdqa_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq A   1 SDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPVNDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKSSWSDHEASSGVSSACPYQGRSSFFRNVVWLIKKNNTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTRLYQNPTTYISVGTSTLNQRLVPKLATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGNCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNS 321
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4kdqb_ B: Influenza hemagglutinin (stalk)                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eeee....hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq B   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain C from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kdqc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq C   1 SDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPVNDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKSSWSDHEASSGVSSACPYQGRSSFFRNVVWLIKKNNTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTRLYQNPTTYISVGTSTLNQRLVPKLATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGNCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNS 321
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 


Chain D from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4kdqd_ D: Influenza hemagglutinin (stalk)                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eeee....hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq D   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain E from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kdqe_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq E   1 SDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPVNDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKSSWSDHEASSGVSSACPYQGRSSFFRNVVWLIKKNNTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTRLYQNPTTYISVGTSTLNQRLVPKLATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPENAYKIVKKGDSTIMKSELEYGNCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNS 321
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 


Chain F from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4kdqf_ F: Influenza hemagglutinin (stalk)                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eeee....hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdq F   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYSE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (2, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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