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(-) Description

Title :  PFA1 FAB COMPLEXED WITH GRIPI PEPTIDE FRAGMENT
 
Authors :  A. S. Gardberg, C. Dealwis
Date :  21 Aug 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L,Q
Keywords :  Immunoglobulin; Alzheimer Disease; Amyloid, 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 LIGHT CHAIN
    Chains: L
    Fragment: LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 2 - IGG2A FAB FRAGMENT HEAVY CHAIN, FD PORTION
    Chains: H
    Fragment: FD PORTION OF HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 3 - GRIPI PEPTIDE FRAGMENT
    Chains: Q
    Engineered: YES
    Fragment: HEXAPEPTIDE
    Synonym: GLUTAMATE RECEPTOR INTERACTING PROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2YCM1Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:176 , SER H:178 , LEU L:159 , SER L:161 , SER L:175 , SER L:176 , THR L:177BINDING SITE FOR RESIDUE GOL L 214
2AC2SOFTWAREGLY L:57 , GLU L:81 , ASP L:82 , HOH L:223BINDING SITE FOR RESIDUE GOL L 215

(-) 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  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:139 -Pro L:140
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2R0Z)

(-) 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:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r0zH01 H:1-113 Immunoglobulins                                                                                            2r0zH02 H:114-212 Immunoglobulins                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee...............eeeee........eeeee.....eeeeeeeeeee.....eeeee.....eeee...ee...eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2r0z H    1 QVTLKESGPGILKPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDDRSYNPSLKSQLTISKDTSRNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGLSSGVHTFPALLQDLYTLSSSSTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E       110       120       135       145       155 ||    166    || 177       187       197       207      
                                                             35A|                                             82A||               100A||||                         128|                    157|         171|                                        
                                                              35B                                              82B|                100B|||                          134                     159          173                                        
                                                                                                                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 d2r0zl1 L:1-106A automated matches                                                                              d2r0zl2 L:107-213 automated matches                                                                         SCOP domains
               CATH domains 2r0zL01 L:1-107 Immunoglobulins                                                                                  -2r0zL02 L:109-208 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r0z L    1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEc  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204        |
                                                     27A||||                                                                            106A                                                                                                        213-YCM
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain Q from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                2r0z Q    2 AKFRHD    7
   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 2R0Z)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (A2NHM3_MOUSE | A2NHM3)

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  2r0z
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  GCAA_MOUSE | P01863
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yec 1yef 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

2ipt 2ipu 2iq9 2iqa 2r0w