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(-) Description

Title :  PFA1 FAB FRAGMENT
 
Authors :  A. S. Gardberg, C. Dealwis
Date :  12 Oct 06  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Wwddd, Cdr, Abeta, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Gardberg, L. T. Dice, S. Ou, R. L. Rich, E. Helmbrecht, J. Ko, R. Wetzel, D. G. Myszka, P. H. Patterson, C. Dealwis
Molecular Basis For Passive Immunotherapy Of Alzheimer'S Disease
Proc. Natl. Acad. Sci. Usa V. 104 15659 2007
PubMed-ID: 17895381  |  Reference-DOI: 10.1073/PNAS.0705888104

(-) Compounds

Molecule 1 - IGG2A FAB FRAGMENT HEAVY CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C
 
Molecule 2 - IGG2A FAB FRAGMENT LIGHT CHAIN KAPPA
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACM1Ligand/IonACETAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL H:127 , CYS H:128 , PRO L:118 , ASN L:209 , CYS L:213 , HOH L:362BINDING SITE FOR RESIDUE ACM L 220

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:133 -L:193

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:139 -Pro L:140
4Ser H:32 -Gly H:33
5Cys H:128 -Gly H:129
6Thr H:131 -Thr H:132
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149
9Ser H:172 -Gly H:173
10Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IPT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IPT)

(-) Exons   (0, 0)

(no "Exon" information available for 2IPT)

(-) 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 H from PDB  Type:PROTEIN  Length:223
 aligned with Q6PIP8_MOUSE | Q6PIP8 from UniProtKB/TrEMBL  Length:464

    Alignment length:226
                                                             54 55                                                            118       119                                                                                                                   
                                    29        39        49    |  |57        67        77        87        97       107       117|        -|      128       138       148       158       168       178       188       198       208       218       228      
        Q6PIP8_MOUSE     20 EVKLEESGGGLVQPGGSMKLSCVASGFTFSNSWMN--WVRQSPEKGLEWVAQIRLRSDNYATHYAESVKGRFTISRDDSKSRLYLQMSSLRAEDTGIYYCT---------NAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  234
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2iptH01 H:1-113 Immunoglobulins                                                                                               2iptH02 H:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.................................---....hhhh........hhh..........hhhhh..................................eeeee..................................hhh.........................................hhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ipt H    1 QVTLKESGPGILKPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDD---KSYNPSLKSQLTISKDAARNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                                    10        20        30     || 38        48       | - |      65        75       82C        92      100B|||    107       117       127       137       147       157       167       177       187       197       207      
                                                             35A|                   56  57                       82A||               100A||||                                                                                                                 
                                                              35B                                                 82B|                100B|||                                                                                                                 
                                                                                                                   82C                 100C||                                                                                                                 
                                                                                                                                        100D|                                                                                                                 
                                                                                                                                         100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  219
               SCOP domains d2iptl1 L:1-106A automated matches                                                                              d2iptl2 L:107-213 automated matches                                                                         SCOP domains
               CATH domains 2iptL01 L:1-107 Immunoglobulins                                                                                  -2iptL02 L:109-208 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........................................................hhhhh.....................................hhhhhhhh......................................................hhhhhhh......................hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ipt L    1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204         
                                                     27A||||                                                                            106A                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:219
                                                                                                                                          113                                                                                                          
                                    10        20        30        40        50        60        70        80        90       100       110  |      -         -         -         -         -         -         -         -         -         -         
         KV2A7_MOUSE      1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIKR----------------------------------------------------------------------------------------------------------    -
               SCOP domains d2iptl1 L:1-106A automated matches                                                                              d2iptl2 L:107-213 automated matches                                                                         SCOP domains
               CATH domains 2iptL01 L:1-107 Immunoglobulins                                                                                  -2iptL02 L:109-208 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........................................................hhhhh.....................................hhhhhhhh......................................................hhhhhhh......................hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ipt L    1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204         
                                                     27A||||                                                                            106A                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E
   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  (2, 2)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IPT)

(-) Gene Ontology  (2, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q6PIP8_MOUSE | Q6PIP8)

Chain L   (KV2A7_MOUSE | P01631)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain L   (A2NHM3_MOUSE | A2NHM3)

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  2ipt
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  GCAB_MOUSE | P01864
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  KV2A7_MOUSE | P01631
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        GCAB_MOUSE | P01864: 1bog 1cfn 1cfq 1cfs 1cft 1hh6 1hh9 1hi6 2iq9 2iqa 2vwe
        KV2A7_MOUSE | P01631: 1bfv 1cfv 1dlf 1maj 1mak 1n4x 1svz 1wz1 2bfv 2dlf 2hkf 2hkh 2iqa 2o5x 2o5y 2o5z 2r0w 2vq1
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 2dqt 2dqu 2dtm 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe
        Q6PIP8_MOUSE | Q6PIP8: 2ai0 2r2h 3j42 4kvc 4pb0

(-) Related Entries Specified in the PDB File

2ipu PFA1 FAB FRAGMENT COMPLEXED WITH ABETA 1-8 PEPTIDE
2iq9 PFA2 FAB FRAGMENT, TRICLINIC APO FORM
2iqa PFA2 FAB FRAGMENT, MONOCLINIC APO FORM
2iqb PFA2 FAB FRAGMENT BOUND TO ABETA 1-8