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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEMAGGLUTININ OF FERRET-TRANSMISSIBLE H5N1 VIRUS IN COMPLEX WITH AVIAN RECEPTOR ANALOG LSTA
 
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 :  2.48
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  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:95 , LEU A:133 , GLY A:134 , VAL A:135 , SER A:136 , SER A:137 , ILE A:155 , HIS A:183 , GLU A:190 , LEU A:194 , HOH A:718 , HOH A:744 , HOH A:756BINDING SITE FOR RESIDUE SIA A 604
2AC2SOFTWARETYR C:95 , LEU C:133 , VAL C:135 , SER C:136 , SER C:137 , LYS C:193 , LEU C:194BINDING SITE FOR RESIDUE SIA C 604
3AC3SOFTWAREGLN A:19 , ASN A:27BINDING SITE FOR MONO-SACCHARIDE NAG A 601 BOUND TO ASN A 27
4AC4SOFTWAREASN A:169 , ASN A:240 , HOH A:705 , SER C:221BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 169 RESIDUES 602 TO 603
5AC5SOFTWAREGLN C:19 , ASN C:27BINDING SITE FOR MONO-SACCHARIDE NAG C 601 BOUND TO ASN C 27
6AC6SOFTWAREASN C:169 , ASN C:240 , ALA C:242BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 169 RESIDUES 602 TO 603
7AC7SOFTWAREGLN E:19 , ASN E:27BINDING SITE FOR MONO-SACCHARIDE NAG E 601 BOUND TO ASN E 27
8AC8SOFTWARESER A:221 , ASN E:169 , ASN E:240 , ALA E:242BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 169 RESIDUES 602 TO 603

(-) 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 4KDN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KDN)

(-) 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 d4kdna_ 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
                 4kdn 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 d4kdnb_ B: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdn 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 d4kdnc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....................eee.ee......eeee.....ee....hhhhhhh................eee...........eee.hhhhhhhhhh...eeeeee..hhhhh.........eeeee....ee....eee..........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
                 4kdn 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 d4kdnd_ D: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdn 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 d4kdne_ E: 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.........eeeee....ee....eee..........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
                 4kdn 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 d4kdnf_ F: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdn 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 4KDN)

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
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    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 4kdo 4n5y 4n5z 4xnm 4xnq 4xrc 5a3i

(-) Related Entries Specified in the PDB File

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