Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FAB CR6261 IN COMPLEX WITH A H5N1 INFLUENZA VIRUS HEMAGGLUTININ.
 
Authors :  D. C. Ekiert, M. A. Elsliger, I. A. Wilson
Date :  20 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,H,I,L,M
Biol. Unit 1:  A,B,H,L  (3x)
Biol. Unit 2:  C,D,I,M  (3x)
Keywords :  Hemagglutinin, Fab, Neutralizing Antibodies, Antibody, Avian Flu, Envelope Protein, Fusion Protein, Viral Protein - Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Ekiert, G. Bhabha, M. A. Elsliger, R. H. Friesen, M. Jongeneelen, M. Throsby, J. Goudsmit, I. A. Wilson
Antibody Recognition Of A Highly Conserved Influenza Virus Epitope.
Science V. 324 246 2009
PubMed-ID: 19251591  |  Reference-DOI: 10.1126/SCIENCE.1171491

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC-HT
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RECEPTOR BINDING DOMAIN, HA1
    Gene: HA, HEMAGGLUTININ (HA)
    Organism Common: A/VIET NAM/1203/2004(H5N1)
    Organism Scientific: INFLUENZA A VIRUS (A/VIET NAM/1203/2004(H5N1))
    Organism Taxid: 284218
    Strain: A/VIETNAM/1203/2004
 
Molecule 2 - HEMAGGLUTININ
    Chains: B, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBAC-HT
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: MEMBRANE FUSION DOMAIN, HA2
    Gene: HA, HEMAGGLUTININ (HA)
    Organism Common: A/VIET NAM/1203/2004(H5N1)
    Organism Scientific: INFLUENZA A VIRUS (A/VIET NAM/1203/2004(H5N1))
    Organism Taxid: 284218
    Strain: A/VIETNAM/1203/2004
 
Molecule 3 - ANTIBODY (FAB)
    Chains: H, I
    Engineered: YES
    Fragment: FAB HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - ANTIBODY (FAB)
    Chains: L, M
    Engineered: YES
    Fragment: FAB LAMBDA LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDHILM
Biological Unit 1 (3x): AB  H L 
Biological Unit 2 (3x):   CD I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:33 , HOH A:344 , HOH A:360BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWARENAG A:2 , ASN A:169 , SER A:221 , ASN A:240 , ASP A:241 , ALA A:242BINDING SITE FOR RESIDUE NAG A 334
03AC3SOFTWARENAG A:334BINDING SITE FOR RESIDUE NAG A 2
04AC4SOFTWAREHIS C:18 , ASN C:20 , ASN C:21 , HIS C:38 , PHE I:54BINDING SITE FOR RESIDUE BMA A 4
05AC5SOFTWAREASN A:158 , GLY L:200 , THR L:204BINDING SITE FOR RESIDUE NAG A 335
06AC6SOFTWAREASP A:27 , ARG A:313 , VAL A:315 , ASN B:104BINDING SITE FOR RESIDUE EDO A 336
07AC7SOFTWAREGLU B:147 , ASN B:154BINDING SITE FOR RESIDUE NAG B 182
08AC8SOFTWAREALA B:36 , ASP B:37 , LYS B:38 , GLU B:39 , ARG B:153 , ASN B:154BINDING SITE FOR RESIDUE GOL B 183
09AC9SOFTWAREHIS A:18 , ASN A:20 , ASN A:21 , HIS A:38 , PHE H:54BINDING SITE FOR RESIDUE BMA C 4
10BC1SOFTWARENAG C:2 , ASN C:169 , SER C:221 , ASN C:240 , ASP C:241 , ALA C:242BINDING SITE FOR RESIDUE NAG C 1
11BC2SOFTWARENAG C:1BINDING SITE FOR RESIDUE NAG C 2
12BC3SOFTWAREGLN C:25 , ASN C:33BINDING SITE FOR RESIDUE NAG C 334
13BC4SOFTWAREVAL C:26 , ASP C:27 , ARG C:313 , LEU C:314 , VAL C:315 , VAL D:100 , ASN D:104BINDING SITE FOR RESIDUE EDO C 335
14BC5SOFTWAREGLU D:147 , GLU D:150 , ASN D:154 , THR D:156BINDING SITE FOR RESIDUE NAG D 182

(-) SS Bonds  (20, 20)

Asymmetric 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
13H:22 -H:92
14H:142 -H:208
15I:22 -I:92
16I:142 -I:208
17L:23 -L:88
18L:134 -L:194
19M:23 -M:88
20M:134 -M:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly H:27 -Pro H:28
2Phe H:148 -Pro H:149
3Glu H:150 -Pro H:151
4Tyr L:140 -Pro L:141
5Gly I:27 -Pro I:28
6Phe I:148 -Pro I:149
7Glu I:150 -Pro I:151
8Tyr M:140 -Pro M:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GBM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GBM)

(-) Exons   (0, 0)

(no "Exon" information available for 3GBM)

(-) 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:324
 aligned with Q6DQ33_9INFA | Q6DQ33 from UniProtKB/TrEMBL  Length:565

    Alignment length:324
                                    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       333    
        Q6DQ33_9INFA     14 VKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  337
               SCOP domains d3gbma_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gbmA01 A:8-56,A:273-324                          3gbmA02 A:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                         3gbmA01 A:8-56,A:273-324                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee..hhhhh.........eeeee....ee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....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
                3gbm A    8 DPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    17        27        37        47        56        66        76       |85        95 |     104       114       124 ||    132 |     141       151       161       171       181       191       201       211       221       231       241       251      260A       270       280       290       300       310       320    
                                                                          55A                          83A           96A                          125A|     133A                                                                                                                            260A                                                                
                                                                                                                                                   125B                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with Q6DQ33_9INFA | Q6DQ33 from UniProtKB/TrEMBL  Length:565

    Alignment length:177
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       
        Q6DQ33_9INFA    347 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISGVK  523
               SCOP domains d3gbmb_ B: Influenza hemagglutinin (stalk)                                                                                                                                        SCOP domains
               CATH domains 3gbmB00 B:1-177  [code=3.90.20.10, no name defined]                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm B    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR  177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain C from PDB  Type:PROTEIN  Length:323
 aligned with Q6DQ33_9INFA | Q6DQ33 from UniProtKB/TrEMBL  Length:565

    Alignment length:323
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334   
        Q6DQ33_9INFA     15 KSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  337
               SCOP domains d3gbmc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3gbmC01 C:9-56,C:273-324                         3gbmC02 C:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                         3gbmC01 C:9-56,C:273-324                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhh.hhhhhhhh.......eee...........eee.hhhhhhhhh..eeeeeeee..hhhhh.........eeeee....ee....eee..............ee......eeeeeeeee..hhhhhhhhhh.....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
                3gbm C    9 PGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP  324
                                    18        28        38        48       |57        67        77      | 86        96|      105       115       125||     133|      142       152       162       172       182       192       202       212       222       232       242       252       261       271       281       291       301       311       321   
                                                                         55A                          83A           96A                          125A|     133A                                                                                                                            260A                                                                
                                                                                                                                                  125B                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with Q6DQ33_9INFA | Q6DQ33 from UniProtKB/TrEMBL  Length:565

    Alignment length:173
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516   
        Q6DQ33_9INFA    347 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEI  519
               SCOP domains d3gbmd_ D: Influenza hemagglutinin (stalk)                                                                                                                                    SCOP domains
               CATH domains 3gbmD00 D:1-173  [code=3.90.20.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm D    1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEI  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gbmH01 H:1-113 Immunoglobulins                                                                                          3gbmH02 H:114-227 Immunoglobulins                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.........eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm H    1 EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122   ||  141       151  |||| 166  ||   177  ||   188       198 |||   211       221 || 
                                                                              52A                            82A||               100A|||                       126|               154|||    169|      180|               200||               223| 
                                                                                                              82B|                100B||                        136                156||     171       182                203|                226 
                                                                                                               82C                 100C|                                            157|                                   205                    
                                                                                                                                    100D                                             162                                                          


Chain I from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gbmI01 I:1-113 Immunoglobulins                                                                                          3gbmI02 I:114-223 Immunoglobulins                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee....eeeeeeee.........eeeeee......eeeeee......eee.......eeeeeehhh.eeeeeee..hhhhheeeeeeee........eeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.hhhhh....eeeeeehhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm I    1 EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSASTKGPSVFPLAPSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV  223
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122     ||140       150   ||||165   ||  176   ||  187       197  |||  210       220   
                                                                              52A                            82A||               100A|||                         128|              154|||    169|      180|               200||                  
                                                                                                              82B|                100B||                          137               156||     171       182                203|                  
                                                                                                               82C                 100C|                                             157|                                   205                  
                                                                                                                                    100D                                              162                                                        


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d3gbml1 L:3-105 automated matches                                                                        d3gbml2 L:108-213 automated matches                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------3gbmL02 L:108-213 Immunoglobulins                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....eeeeeee..........eeeeee......eeee..............eee....eeeeeee..hhhhheeeeeeeee..........eeee.........ee..hhhhhhh..eeeeeeeeee.....eeeeee.eeee...eee..........eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm L    3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRTAYVVFGGGTKLTQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  213
                                  ||13        23    ||  31        41        51        61        71        81        91 ||||  100    || 112       122       132       142       152       162       173       183       193      |205        
                                  9|              27A|                                                                93|||       105|                                                           170|                         200|          
                                  11               27B                                                                95A||        108                                                            172                          203          
                                                                                                                       95B|                                                                                                                 
                                                                                                                        95C                                                                                                                 


Chain M from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                      
               SCOP domains d3gbmm1 M:3-106A automated matches                                                                         d3gbmm2 M:112-211 automated matches                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------3gbmM02 M:106-211 Immunoglobulins                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.....eee...eeee...........hhhhhhh..eeeeeeeeee.............eee...ee.....eeeeeeeeehhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gbm M    3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRTAYVVFGGGTKLTVLAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKAAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHESTVEKTVAP  211
                                  ||13        23    ||  31        41        51        61        71        81        91 ||||  100      |114       124       134       144     ||160       171       181       191       204       
                                  9|              27A|                                                                93|||        106A|                                   150|        168|                          199|        
                                  11               27B                                                                95A||          112                                    157         170                           203        
                                                                                                                       95B|                                                                                                      
                                                                                                                        95C
   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  (4, 8)

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

(-) CATH Domains  (4, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GBM)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6DQ33_9INFA | Q6DQ33)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
    Glu I:150 - Pro I:151   [ RasMol ]  
    Gly H:27 - Pro H:28   [ RasMol ]  
    Gly I:27 - Pro I:28   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Phe I:148 - Pro I:149   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr M:140 - Pro M:141   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3gbm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q6DQ33_9INFA | Q6DQ33
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q6DQ33_9INFA | Q6DQ33
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GBM)