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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-META I RHODOPSIN FAB FRAGMENT K42-41L
 
Authors :  C. L. Piscitelli, T. E. Angel, B. W. Bailey, C. M. Lawerence
Date :  17 Sep 04  (Deposition) - 27 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Keywords :  Meta-I, Rhodopsin, Fab, Igg, K42-41L, Phage Display, Antibody, Immunoglobulin, Antibody Imprinting, Peptide Mimetics, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Piscitelli, T. E. Angel, B. W. Bailey, P. Hargrave, E. A. Dratz, C. M. Lawrence
Equilibrium Between Metarhodopsin-I And Metarhodopsin-Ii Is Dependent On The Conformation Of The Third Cytoplasmic Loop.
J. Biol. Chem. V. 281 6813 2006
PubMed-ID: 16407202  |  Reference-DOI: 10.1074/JBC.M510175200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - K42-41L FAB LIGHT CHAIN
    Chains: L, M
    Fragment: ANITGEN BINDING FRAGMENT, FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SP2/0 MOUSE MYELOMA CELLS FUSED WITH IMMUNIZED MOUSE SPLENOCYTES
 
Molecule 2 - K42-41L FAB HEAVY CHAIN
    Chains: H, I
    Fragment: ANTIGEN BINDING FRAGMENT, FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SP2/0 MOUSE MYELOMA CELLS FUSED WITH IMMUNIZED MOUSE SPLENOCYTES
 
Molecule 3 - RHODOPSIN EPITOPE MIMETIC PEPTIDE
    Chains: P, Q
    Engineered: YES
    Fragment: PHAGE DISPLAY CONSENSUS PEPTIDE
    Other Details: CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HILMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  I M Q

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XGY)

(-) Sites  (0, 0)

(no "Site" information available for 1XGY)

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1His L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Trp H:188 -Pro H:189
6His M:94 -Pro M:95
7Tyr M:140 -Pro M:141
8Phe I:146 -Pro I:147
9Glu I:148 -Pro I:149
10Trp I:188 -Pro I:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XGY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XGY)

(-) Exons   (0, 0)

(no "Exon" information available for 1XGY)

(-) 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 H from PDB  Type:PROTEIN  Length:216
 aligned with Q6PF95_MOUSE | Q6PF95 from UniProtKB/TrEMBL  Length:464

    Alignment length:218
                                                                                                                              118                                                                                                                     
                                                                                                                           117  |                                                                                                                     
                                    29        39        49        59        69        79        89        99       109       | -|      127       137       147       157       167       177       187       197       207       217       227        
         Q6PF95_MOUSE    20 QVQLKQSGAELVRPGASVKLSCKASGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAFMQLSSLKSEDSAVYFCAY--GYDALYWGQGTPITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPVVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 235
               SCOP domains ---------------------------------------------------------------------------------------------------------------------d1xgyh1 H:114-21  4 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1xgyH01 H:1-114 Immunoglobulins                                                                                       1xgyH02 H:115-2  14 Immunoglobulins                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.......ee...eeeee........eeeee.....--...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xgy H   1 QVQLQQSGPELVRPGASVKISCKASGYTFTDYYINWVKQRPGQGLEWIGWIFPRNGNTKYNEKFKGKATLTVDKSSSTAFMQLSSLTSEDSAVYFCATTVSYVMDYWGQGTTVTVSSAKTTPPSVYPLAPGSA--TNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126  |  | 136       146       156       166       176       186       196       206        
                                                                              52A                            82A||                                            129  |                                                                                  
                                                                                                              82B|                                               132                                                                                  
                                                                                                               82C                                                                                                                                    


Chain I from PDB  Type:PROTEIN  Length:215
 aligned with Q6PF95_MOUSE | Q6PF95 from UniProtKB/TrEMBL  Length:464

    Alignment length:218
                                                                                                                              118                                                                                                                     
                                                                                                                           117  |                                                                                                                     
                                    29        39        49        59        69        79        89        99       109       | -|      127       137       147       157       167       177       187       197       207       217       227        
         Q6PF95_MOUSE    20 QVQLKQSGAELVRPGASVKLSCKASGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAFMQLSSLKSEDSAVYFCAY--GYDALYWGQGTPITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPVVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 235
               SCOP domains ---------------------------------------------------------------------------------------------------------------------d1xgyi1 I:114-21   4 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 1xgyI01 I:1-114 Immunoglobulins                                                                                       1xgyI02 I:115-2   14 Immunoglobulins                                                                 CATH domains
           Pfam domains (1) V-set-1xgyI03 I:1-111                                                                                              --------------C1-s   et-1xgyI01 I:126-207                                                       ------- Pfam domains (1)
           Pfam domains (2) V-set-1xgyI04 I:1-111                                                                                              --------------C1-s   et-1xgyI02 I:126-207                                                       ------- Pfam domains (2)
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee..eeeeeeeeee....eeee.hhhh..eeeeee....eeeeee........eeeeeee.......ee...eeeee........eeeee.....---..eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xgy I   1 QVQLQQSGPELVRPGASVKISCKASGYTFTDYYINWVKQRPGQGLEWIGWIFPRNGNTKYNEKFKGKATLTVDKSSSTAFMQLSSLTSEDSAVYFCATTVSYVMDYWGQGTTVTVSSAKTTPPSVYPLAPGSA---NSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126  |   |136       146       156       166       176       186       196       206        
                                                                              52A                            82A||                                            129 133                                                                                 
                                                                                                              82B|                                                                                                                                    
                                                                                                               82C                                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1xgyL01 L:1-108 Immunoglobulins                                                                                  1xgyL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.............eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...ee..........eeeee....hhhhh.eeeeeeeeeee....eeeeeee...ee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xgy L   1 DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSNGITYLYWYLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTDFALRISRVEAEDVGVYYCGQMLEHPLTFGTGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E                                                                                                                                                                                        


Chain M from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1xgyM01 M:1-108 Immunoglobulins                                                                                  1xgyM02 M:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.............eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...............eeeee....hhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xgy M   1 DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSNGITYLYWYLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTDFALRISRVEAEDVGVYYCGQMLEHPLTFGTGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E                                                                                                                                                                                        


Chain P from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author hhhhhh Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1xgy P   1 TGALQE   6


Chain Q from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author hhhhhh Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1xgy Q   1 TGALQE   6
   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  (1, 2)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1xgyL02L:109-211
1b1xgyH02H:115-214
1c1xgyI02I:115-214
1d1xgyL01L:1-108
1e1xgyM01M:1-108
1f1xgyM02M:109-211
1g1xgyH01H:1-114
1h1xgyI01I:1-114

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1XGY)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu I:148 - Pro I:149   [ RasMol ]  
    His L:94 - Pro L:95   [ RasMol ]  
    His M:94 - Pro M:95   [ RasMol ]  
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    Tyr M:140 - Pro M:141   [ RasMol ]  
 
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 Related Entries

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        Q6PF95_MOUSE | Q6PF95: 1ejo 1jn6 2a6k 2gsi

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