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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 3.1
 
Authors :  C. Dreyfus
Date :  26 Mar 14  (Deposition) - 21 May 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,I,J
Biol. Unit 1:  I,J  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Immunoglobulin Fab Fragment, Neutralizing Antibody, Hemagglutinin Glycoproteins, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wyrzucki, C. Dreyfus, I. Kohler, M. Steck, I. A. Wilson, L. Hangartner
Alternative Recognition Of The Conserved Stem Epitope In Influenza A Virus Hemagglutinin By A Vh3-30-Encoded Heterosubtypic Antibody.
J. Virol. V. 88 7083 2014
PubMed-ID: 24719426  |  Reference-DOI: 10.1128/JVI.00178-14

(-) Compounds

Molecule 1 - ANTIBODY 3.1 HEAVY CHAIN
    Chains: I, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY 3.1 LIGHT CHAIN
    Chains: J, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABIJ
Biological Unit 1 (1x):   IJ
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4PY7)

(-) Sites  (0, 0)

(no "Site" information available for 4PY7)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:141 -A:197
3B:23 -B:88
4B:134 -B:194
5I:22 -I:95
6I:144 -I:200
7J:23 -J:88
8J:134 -J:194

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Asn I:56 -Lys I:57
2Gly I:101 -Tyr I:102
3Phe I:150 -Pro I:151
4Glu I:152 -Pro I:153
5Ser J:7 -Pro J:8
6Phe J:94 -Pro J:95
7Tyr J:140 -Pro J:141
8Ala J:144 -Lys J:145
9Gly A:98 -Tyr A:99
10Phe A:147 -Pro A:148
11Glu A:149 -Pro A:150
12Ser B:7 -Pro B:8
13Phe B:94 -Pro B:95
14Tyr B:140 -Pro B:141
15Ala B:144 -Lys B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PY7)

(-) Exons   (0, 0)

(no "Exon" information available for 4PY7)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee.....eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee...........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4py7 A   1 QVQLVQSGGGVVQPGRSLRLSCAASEFTFRMYATHWVRQAPGKGLEWVALISYDGSNKYYADSVKGRFTISRDNSMNTVYLQMNTLRPEDTAVYYCARDLGGYFIRGIMDVWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 215
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126     ||139       149       159       169       179       189       199       209      
                                                                              52A                            82A||                                               132|                                                                               
                                                                                                              82B|                                                136                                                                               
                                                                                                               82C                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee......eeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py7 B   1 ELQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain I from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py7 I   1 QVQLVQSGGGVVQPGRSLRLSCAASEFTFRMYATHWVRQAPGKGLEWVALISYDGSNKYYADSVKGRFTISRDNSMNTVYLQMNTLRPEDTAVYYCARDLGGYFIRGIMDVWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 218
                                    10        20        30        40        50  |     59        69        79        89        99       109       119       129    || 143       153       163       173       183       193       203       213     
                                                                              52A                                                                               134|                                                                               
                                                                                                                                                                 139                                                                               


Chain J from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee......eeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py7 J   1 ELQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (0, 0)

(no "SCOP Domain" information available for 4PY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PY7)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PY7)

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  Cis Peptide Bonds
    Ala B:144 - Lys B:145   [ RasMol ]  
    Ala J:144 - Lys J:145   [ RasMol ]  
    Asn I:56 - Lys I:57   [ RasMol ]  
    Glu A:149 - Pro A:150   [ RasMol ]  
    Glu I:152 - Pro I:153   [ RasMol ]  
    Gly A:98 - Tyr A:99   [ RasMol ]  
    Gly I:101 - Tyr I:102   [ RasMol ]  
    Phe A:147 - Pro A:148   [ RasMol ]  
    Phe B:94 - Pro B:95   [ RasMol ]  
    Phe I:150 - Pro I:151   [ RasMol ]  
    Phe J:94 - Pro J:95   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser J:7 - Pro J:8   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr J:140 - Pro J:141   [ RasMol ]  
 
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4py8