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(-) Description

Title :  STRUCTURE OF THE BROADLY NEUTRALIZING ANTIBODY AP33
 
Authors :  J. A. Potter, A. Owsianka, N. Jeffery, D. Matthews, Z. Keck, P. Lau, S. K. G. L. Taylor, A. H. Patel
Date :  26 Jul 12  (Deposition) - 10 Oct 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Antibody Fab, Neutralizing Antibody, Hcv E2, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Potter, A. M. Owsianka, N. Jeffery, D. J. Matthews, Z. Y. Keck, P. Lau, S. K. Foung, G. L. Taylor, A. H. Patel
Toward A Hepatitis C Virus Vaccine: The Structural Basis Of Hepatitis C Virus Neutralization By Ap33, A Broadly Neutralizing Antibody.
J. Virol. V. 86 12923 2012
PubMed-ID: 22993159  |  Reference-DOI: 10.1128/JVI.02052-12

(-) Compounds

Molecule 1 - NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
    Chains: H, A
    Fragment: FAB FRAGMENT OF AP33 HEAVY CHAIN
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
    Chains: L, B
    Fragment: FAB FRAGMENT OF AP33 LIGHT CHAIN
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:33 , TYR A:50 , PHE B:32 , ASN B:91 , TRP B:96 , TYR L:28BINDING SITE FOR RESIDUE PGE A 301
2AC2SOFTWARETYR B:28 , TYR H:50 , ASN L:91 , TRP L:96BINDING SITE FOR RESIDUE PGE B 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:195
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:195
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Asn L:1 -Ile L:2
5Ser L:7 -Pro L:8
6Asp L:76 -Pro L:77
7Asp L:94 -Pro L:95
8Tyr L:140 -Pro L:141
9Phe A:146 -Pro A:147
10Glu A:148 -Pro A:149
11Trp A:188 -Pro A:189
12Ser B:7 -Pro B:8
13Asp B:76 -Pro B:77
14Asp B:94 -Pro B:95
15Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GAY)

(-) 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:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...ee.....eeeeee........eeeeee.....eeeeeee.....eee.hhhh....eee.....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.........ee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gay A    2 VQLQESGPSLVKPSQTLSLTCSVTGDSITYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTSVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP  212
                                    11        21        33        43        53        63        73       82A||      90       100||     108       118       135       145       155       165       175       185       195       205       
                                                       30|                                               82A||               100A|                       126|                                                                              
                                                        33                                                82B|                100B                        134                                                                              
                                                                                                           82C                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains d4gayb1 B:1-107 automated matches                                                                              d4gayb2 B:108-212 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4gay B    1 NIVLTQSPVSLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                     27A|||                                                                                                                                                                                         
                                                      27B||                                                                                                                                                                                         
                                                       27C|                                                                                                                                                                                         
                                                        27D                                                                                                                                                                                         


Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeee........eeeeeee.....eeeeeeee....eee.hhhhh.eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gay H    2 VQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    11        21        31        41        51        61        71        81 |||    88        98  ||   106       116       126||     141       151       161       171       181       191       201       211  
                                                                                                           82A||               100A|                        127|                                                                                
                                                                                                            82B|                100B                         133                                                                                
                                                                                                             82C                                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4gayl1 L:1-107 automated matches                                                                              d4gayl2 L:108-211 automated matches                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...........eeeeee......ee.ee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee......eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gay L    1 NIVLTQSPVSLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSENGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       158       168       178       188       198       208   
                                                     27A|||                                                                                                                            154|                                                      
                                                      27B||                                                                                                                             157                                                      
                                                       27C|                                                                                                                                                                                      
                                                        27D
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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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  4gay
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(-) Related Entries Specified in the PDB File

4gag THE SAME ANTIBODY COMPLEXED WITH A PEPTIDE
4gaj THE SAME ANTIBODY COMPLEXED WITH A PEPTIDE