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(-) Description

Title :  REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING
 
Authors :  W. I. Weis, A. T. Bruenger, J. J. Skehel, D. C. Wiley
Date :  11 Sep 89  (Deposition) - 15 Jan 91  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Influenza Virus Hemagglutinin, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. I. Weis, A. T. Brunger, J. J. Skehel, D. C. Wiley
Refinement Of The Influenza Virus Hemagglutinin By Simulate Annealing.
J. Mol. Biol. V. 212 737 1990
PubMed-ID: 2329580  |  Reference-DOI: 10.1016/0022-2836(90)90234-D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (A/AICHI/2/1968(H3N2))
    Organism Taxid: 387139
    Strain: (A/AICHI/2/1968(H3N2))
    Synonym: HEMAGGLUTININ
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (A/AICHI/2/1968(H3N2))
    Organism Taxid: 387139
    Strain: (A/AICHI/2/1968(H3N2))
    Synonym: HEMAGGLUTININ

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1MAN3Ligand/IonALPHA-D-MANNOSE
2NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:98 , GLY A:135 , SER A:136 , ASN A:137 , TRP A:153 , THR A:155 , GLU A:190 , LEU A:194 , LEU A:226 , SER A:228BINDING SITE FOR RESIDUE SIA A 329
02AC2SOFTWAREASN A:38 , THR A:318 , LEU B:52BINDING SITE FOR RESIDUE NAG A 330
03AC3SOFTWAREGLN A:80 , ASN A:81 , PHE A:120BINDING SITE FOR RESIDUE NAG A 334
04AC4SOFTWAREASN A:165 , THR A:167 , NAG A:340 , SER E:219BINDING SITE FOR RESIDUE NAG A 339
05AC5SOFTWARENAG A:339 , MAN A:341 , PRO E:221 , TRP E:222BINDING SITE FOR RESIDUE NAG A 340
06AC6SOFTWARENAG A:340 , TRP E:222BINDING SITE FOR RESIDUE MAN A 341
07AC7SOFTWARESER A:45 , ASN A:285 , VAL A:297 , ASN A:298BINDING SITE FOR RESIDUE NAG A 348
08AC8SOFTWAREALA B:147 , GLU B:150 , ASN B:154 , THR B:156BINDING SITE FOR RESIDUE NAG B 401
09AC9SOFTWARETYR C:98 , GLY C:135 , SER C:136 , ASN C:137 , TRP C:153 , THR C:155 , GLU C:190 , LEU C:194 , LEU C:226 , SER C:228BINDING SITE FOR RESIDUE SIA C 329
10BC1SOFTWAREASN C:38 , THR C:318 , LEU D:52BINDING SITE FOR RESIDUE NAG C 330
11BC2SOFTWAREGLN C:80 , ASN C:81 , PHE C:120BINDING SITE FOR RESIDUE NAG C 334
12BC3SOFTWARESER A:219 , ASN C:165 , THR C:167 , NAG C:340BINDING SITE FOR RESIDUE NAG C 339
13BC4SOFTWAREPRO A:221 , TRP A:222 , NAG C:339 , MAN C:341BINDING SITE FOR RESIDUE NAG C 340
14BC5SOFTWARETRP A:222 , NAG C:340BINDING SITE FOR RESIDUE MAN C 341
15BC6SOFTWARESER C:45 , ASN C:285 , VAL C:297 , ASN C:298BINDING SITE FOR RESIDUE NAG C 348
16BC7SOFTWAREALA D:147 , GLU D:150 , ASN D:154 , THR D:156BINDING SITE FOR RESIDUE NAG D 401
17BC8SOFTWARETYR E:98 , GLY E:135 , SER E:136 , ASN E:137 , TRP E:153 , THR E:155 , GLU E:190 , LEU E:194 , LEU E:226 , SER E:228BINDING SITE FOR RESIDUE SIA E 329
18BC9SOFTWAREASN E:38 , THR E:318 , LEU F:52BINDING SITE FOR RESIDUE NAG E 330
19CC1SOFTWAREGLN E:80 , ASN E:81 , PHE E:120BINDING SITE FOR RESIDUE NAG E 334
20CC2SOFTWARESER C:219 , ASN E:165 , THR E:167 , NAG E:340 , SER F:29BINDING SITE FOR RESIDUE NAG E 339
21CC3SOFTWAREPRO C:221 , TRP C:222 , NAG E:339 , MAN E:341BINDING SITE FOR RESIDUE NAG E 340
22CC4SOFTWARETRP C:222 , NAG E:340BINDING SITE FOR RESIDUE MAN E 341
23CC5SOFTWARESER E:45 , ASN E:285 , VAL E:297 , ASN E:298BINDING SITE FOR RESIDUE NAG E 348
24CC6SOFTWAREALA F:147 , GLU F:150 , ASN F:154 , THR F:156BINDING SITE FOR RESIDUE NAG F 401

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7C:14 -D:137
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:144 -D:148
13E:14 -F:137
14E:52 -E:277
15E:64 -E:76
16E:97 -E:139
17E:281 -E:305
18F:144 -F:148

(-) 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 5HMG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HMG)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5hmga_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------5hmgA01 A:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   -------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee................................................hhhhhh.................................hhhhhhhhhhh...eee..............................eee.........eeeeeee.....eeeeeeeee...hhhhhhh......eeeee....eeee...............eeeeeeeee...eeeeeee...eeeeeeeee..................................................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg A   1 QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQT 328
                                    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:175
                                                                                                                                                                                                               
               SCOP domains d5hmgb_ B: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains 5hmgB00 B:1-175  [code=3.90.20.10, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee.....hhhhhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg B   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTGSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain C from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5hmgc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------5hmgC01 C:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   -------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee................................................hhhhhh.................................hhhhhhhhhhh...eee..............................eee.........eeeeeee.....eeeeeeeee...hhhhhhh......eeeee....eeee...............eeeeeeeee...eeeeeee...eeeeeeeee..................................................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg C   1 QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQT 328
                                    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:175
                                                                                                                                                                                                               
               SCOP domains d5hmgd_ D: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains 5hmgD00 D:1-175  [code=3.90.20.10, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee.....hhhhhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg D   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTGSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain E from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5hmge_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------5hmgE01 E:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   -------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee................................................hhhhhh.................................hhhhhhhhhhh...eee..............................eee.........eeeeeee.....eeeeeeeee...hhhhhhh......eeeee....eeee...............eeeeeeeee...eeeeeee...eeeeeeeee..................................................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg E   1 QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQT 328
                                    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:175
                                                                                                                                                                                                               
               SCOP domains d5hmgf_ F: Influenza hemagglutinin (stalk)                                                                                                                                      SCOP domains
               CATH domains 5hmgF00 F:1-175  [code=3.90.20.10, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee.....hhhhhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hmg F   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTGSEMNKLFEKTRRQLRENAEEMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKG 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hmg
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  HEMA_I68A0 | P03437
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMA_I68A0 | P03437: 1eo8 1fyt 1ha0 1hgd 1hge 1hgf 1hgg 1hgh 1hgi 1hgj 1htm 1j8h 1ken 1kg0 1pyw 1qfu 1qu1 2hmg 2vir 2vis 2vit 2viu 2ypg 3eym 3hmg 3s4s 3s5l 3vun 3ztj 4c56 4hmg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HMG)