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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEMAGGLUTININ OF FERRET-TRANSMISSIBLE H5N1 VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOG LSTC
 
Authors :  X. Lu, Y. Shi, W. Zhang, Y. Zhang, J. Qi, G. F. Gao
Date :  25 Apr 13  (Deposition) - 24 Jul 13  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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 17-337
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 284218
    Strain: (A/VIET NAM/1203/2004(H5N1))
 
Molecule 2 - HEMAGGLUTININ
    Chains: B, D, F
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: RESIDUES 347-521
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 284218
    Strain: (A/VIET NAM/1203/2004(H5N1))

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:169 , ASN A:240 , ASP A:241 , ALA A:242 , NAG A:402 , HOH A:546 , HOH A:569BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARENAG A:401 , HOH A:508 , HOH A:509BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWARETYR A:95 , LEU A:133 , VAL A:135 , SER A:136 , SER A:137 , ILE A:155 , HIS A:183 , GLU A:190 , LEU A:194 , LEU A:226 , HOH A:510 , HOH A:520BINDING SITE FOR RESIDUE SIA A 403
04AC4SOFTWAREGLN C:19 , ASN C:27BINDING SITE FOR RESIDUE NAG C 601
05AC5SOFTWAREASN C:169 , ASN C:240 , ALA C:242 , NAG C:603 , HOH C:745 , SER E:221BINDING SITE FOR RESIDUE NAG C 602
06AC6SOFTWARENAG C:602BINDING SITE FOR RESIDUE NAG C 603
07AC7SOFTWARETYR C:95 , LEU C:133 , VAL C:135 , SER C:136 , SER C:137 , ILE C:155 , HIS C:183 , GLU C:190 , LEU C:194 , GAL C:605 , HOH C:733BINDING SITE FOR RESIDUE SIA C 604
08AC8SOFTWAREGLY C:225 , LEU C:226 , SIA C:604 , NAG C:606 , HOH C:729BINDING SITE FOR RESIDUE GAL C 605
09AC9SOFTWAREGAL C:605BINDING SITE FOR RESIDUE NAG C 606
10BC1SOFTWAREASN E:169 , ASN E:240 , NAG E:402 , HOH E:548BINDING SITE FOR RESIDUE NAG E 401
11BC2SOFTWARENAG E:401BINDING SITE FOR RESIDUE NAG E 402

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:8 -B:471
2A:46 -A:278
3A:59 -A:71
4A:94 -A:139
5A:282 -A:306
6B:478 -B:482
7C:8 -D:471
8C:46 -C:278
9C:59 -C:71
10C:94 -C:139
11C:282 -C:306
12D:478 -D:482
13E:8 -F:471
14E:46 -E:278
15E:59 -E:71
16E:94 -E:139
17E:282 -E:306
18F:478 -F:482

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val B:400 -Gly B:401
2Val D:400 -Gly D:401
3Val F:400 -Gly F:401

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KDO)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kdoa_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhh................eee...........eee.hhhhhhhhhh...eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhh......eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeee......eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdo A   4 QDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLAIGLRNSP 325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains d4kdob_ B: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdo B 335 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISG 509
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504     


Chain C from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kdoc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......ee.......ee...eee.ee......eeee.....ee....hhhhhhh................eee...........eee.hhhhhhhhhh...eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhh......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
                 4kdo C   4 QDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLAIGLRNSP 325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains d4kdod_ D: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.......eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdo D 335 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISG 509
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504     


Chain E from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kdoe_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhh................eee...........eee.hhhhhhhhhh...eeeeee..hhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhh......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
                 4kdo E   4 QDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLAIGLRNSP 325
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  


Chain F from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains d4kdof_ F: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdo F 335 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISG 509
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
   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 4KDO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Val B:400 - Gly B:401   [ RasMol ]  
    Val D:400 - Gly D:401   [ RasMol ]  
    Val F:400 - Gly F:401   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6DQ33_9INFA | Q6DQ33: 3fku 4mhh
UniProtKB/TrEMBL
        Q6DQ33_9INFA | Q6DQ33: 3gbm 4fqi 4kdm 4kdn 4n5y 4n5z 4xnm 4xnq 4xrc 5a3i

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