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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 39.29 IN COMPLEX WITH INFLUENZA HEMAGGLUTININ A/PERTH/16/2009 (H3N2)
 
Authors :  R. Fong, L. R. Swem, P. J. Lupardus
Date :  22 May 13  (Deposition) - 07 Aug 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Igg, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Nakamura, N. Chai, S. Park, N. Chiang, Z. Lin, H. Chiu, R. Fong, D. Yan J. Kim, J. Zhang, W. P. Lee, A. Estevez, M. Coons, M. Xu, P. Lupardus, M. Balazs, L. R. Swem
A Novel In Vivo Human Plasmablast Enrichment Technique Allows Rapid Identification Of Therapeutic Anti-Influenza A Antibodies
Cell Host Microbe V. 14 93 2013
PubMed-ID: 23870317  |  Reference-DOI: 10.1016/J.CHOM.2013.06.004

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: TNI
    Expression System Taxid: 7108
    Fragment: EXTRACELLULAR HA0 FRAGMENT
    Gene: HA, HEMAGGLUTININ
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 654811
    Strain: A/PERTH/16/2009(H3N2)
 
Molecule 2 - HUMAN IGG HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HUMAN IGG LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:40 , THR A:53 , ASN A:54 , NAG A:602 , PRO H:101 , PHE H:103 , GLY H:104BINDING SITE FOR RESIDUE NAG A 601
02AC2SOFTWARENAG A:601 , BMA A:603 , TYR H:111 , TYR L:49BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWARENAG A:602BINDING SITE FOR RESIDUE BMA A 603
04AC4SOFTWAREASN A:79 , TYR A:110BINDING SITE FOR RESIDUE NAG A 604
05AC5SOFTWAREASN A:142 , THR A:144BINDING SITE FOR RESIDUE NAG A 605
06AC6SOFTWAREGLN A:148 , ASN A:149BINDING SITE FOR RESIDUE NAG A 606
07AC7SOFTWAREASN A:181 , THR A:183 , SER A:235 , NAG A:608 , NAG A:610BINDING SITE FOR RESIDUE NAG A 607
08AC8SOFTWAREARG A:238 , NAG A:607 , BMA A:609BINDING SITE FOR RESIDUE NAG A 608
09AC9SOFTWARENAG A:608BINDING SITE FOR RESIDUE BMA A 609
10BC1SOFTWAREALA A:179 , ASN A:181 , ASN A:262 , NAG A:607 , NAG A:611BINDING SITE FOR RESIDUE NAG A 610
11BC2SOFTWAREASP A:204 , NAG A:610BINDING SITE FOR RESIDUE NAG A 611
12BC3SOFTWAREASN A:301 , ASN A:314BINDING SITE FOR RESIDUE NAG A 612
13BC4SOFTWAREASN A:499 , THR A:501BINDING SITE FOR RESIDUE NAG A 613
14BC5SOFTWAREASN A:47 , ASP A:48 , GLN A:49 , VAL L:28 , HIS L:31 , SER L:67 , GLY L:68BINDING SITE FOR RESIDUE PO4 L 301
15BC6SOFTWAREALA L:9 , TYR L:87 , GLY L:100BINDING SITE FOR RESIDUE PGE L 302

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:482
2A:68 -A:293
3A:80 -A:92
4A:113 -A:155
5A:297 -A:321
6A:489 -A:493
7H:22 -H:96
8H:152 -H:208
9L:23 -L:88
10L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:70 -Pro A:71
2Thr H:147 -Ala H:148
3Phe H:158 -Pro H:159
4Glu H:160 -Pro H:161
5Ser L:7 -Pro L:8
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KVN)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4kvna1 A:27-343 Hemagglutinin                                                                                                                                                                                                                                                                                               d4kvna2 A:355-517 automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeee......eeee....eeeee..eee..eee.....ee...........ee......eee.............ee.......eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...eee.....hhhhhhhhhh.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvn A  27 ATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILDGKNCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSKNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQASGRITVSTKRSQQTVSPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQ 517
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      |357       367       377       387       397       407       427       437       447       457       467       477       487       497       507       517
                                                                                                                                                                                                                                                                                                                                                      343|                                                         415|                                                                                           
                                                                                                                                                                                                                                                                                                                                                       355                                                          426                                                                                           


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eee......eeeee.......eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee......eeeeeeeee....eeeee.........ee...ee.....eeeeeeee............eeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kvn H   2 VQLVESGGGVVQPGKSPRLSCAASGSSYAVHWVRQAPGKGLEWVTLISYDGANQYYADSVKGRFTISRDNSKNTVYLQMNSLRPEDTAVYYCAVPGPVFGIFPPWSYFDNWGQGILVTVSSASTKGPSVFPLAPSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 226
                                    11        21    ||  34        44        54        64        74        84        94       104       114       124       134     ||150       160       170       180       190       200       210       220      
                                                   26|                                                                                                           140|                                                                               
                                                    30                                                                                                            147                                                                               


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4kvnl1 L:2-106 automated matches                                                                          d4kvnl2 L:107-212 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvn L   2 IVLTQSPATLSVSPGERATLSCRASQVISHNLAWYQQKPGQAPRLLIYGASTRASGIPARFSGSGSGTDYTLTITSLQPEDFAVYYCQHYSNWPPRLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    11        21        31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199       209   
                                                                                                                        95A|                                                                                                                     
                                                                                                                         95B
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:160 - Pro H:161   [ RasMol ]  
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    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr H:147 - Ala H:148   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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