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(-) Description

Title :  PFA1 FAB FRAGMENT COMPLEXED WITH PYRO-GLU3-A-BETA (3-8)
 
Authors :  A. S. Gardberg, C. G. Dealwis
Date :  21 Oct 08  (Deposition) - 12 May 09  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  H,L,Q
Keywords :  Fab, Amyloid, Alzheimer'S, Protein-Peptide Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gardberg, L. Dice, K. Pridgen, J. Ko, P. Patterson, S. Ou, R. Wetzel, C. Dealwis
Structures Of Abeta-Related Peptide--Monoclonal Antibody Complexes.
Biochemistry V. 48 5210 2009
PubMed-ID: 19385664  |  Reference-DOI: 10.1021/BI9001216

(-) Compounds

Molecule 1 - IF KAPPA LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Strain: BALB C
    Expression System Taxid: 10090
    Gene: IGK-C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PFA1 FAB LIGHT CHAIN
 
Molecule 2 - PFA1 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Strain: BALB C
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PYRO-GLU3-A-BETA (3-8) PEPTIDE
    Chains: Q
    Engineered: YES
    Other Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. IT IS IDENTICAL TO FRAGMENT FROM HOMO SAPIENS AMYLOID BETA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLQ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3YCM1Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:57 , ARG H:59 , SER H:72 , LYS H:73 , ASP L:115BINDING SITE FOR RESIDUE GOL H 224

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:97
2H:150 -H:205
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:156 -Pro H:157
5Glu H:158 -Pro H:159
6Trp H:198 -Pro H:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EYS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EYS)

(-) Exons   (0, 0)

(no "Exon" information available for 3EYS)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eysH01 H:1-123 Immunoglobulins                                                                                            3eysH02 H:124-222 Immunoglobulins                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.hhhhh.eeeeee....eeeeee...hhhhheeeeeee.................eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee.......eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eys H   1 AVTLKESGPGILKPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDDRSYNPSLKSQLTISKDAARNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176   ||  188       198       208       218     
                                                                                                                                                                  137|                                 180|                                        
                                                                                                                                                                   144                                  183                                        


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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eys L   1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEc 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        |
                                                                                                                                                                                                                                                    219-YCM


Chain Q from PDB  Type:PROTEIN  Length:5
                                     
               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
                 3eys Q   3 xFRHD   7
                            |    
                            3-PCA
   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 3EYS)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EYS)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3EYS)

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  Cis Peptide Bonds
    Glu H:158 - Pro H:159   [ RasMol ]  
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    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:198 - Pro H:199   [ RasMol ]  
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    Val L:99 - Pro L:100   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
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 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

3eyu PFA1 FAB FRAGMENT COMPLEXED WITH ROR2(518-525)