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(-) Description

Title :  THE STRUCTURE OF FAB WITH INTERMEDIATE AFFINITY FOR FLUORESCEIN.
 
Authors :  S. Terzyan, P. A. Ramsland, E. W. Voss Jr. , J. N. Herron, A. B. Edmundson
Date :  05 May 04  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  C,D,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody, Fab, Fluorescein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Terzyan, P. A. Ramsland, E. W. Voss Jr. , J. N. Herron, A. B. Edmundson
Three-Dimensional Structures Of Idiotypically Related Fabs With Intermediate And High Affinity For Fluorescein.
J. Mol. Biol. V. 339 1141 2004
PubMed-ID: 15178254  |  Reference-DOI: 10.1016/J.JMB.2004.03.080
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN
    Cell: LYMPHOCYTE-PLASMA CELL
    Cell Line: 9-40 MURINE-MURINE HYBRIDOMA
    Chains: L, C
    Fragment: FAB
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
    Variant: BALB/CV
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN
    Cell: LYMPHOCYTE-PLASMA CELL
    Cell Line: 9-40 MURINE-MURINE HYBRIDOMA
    Chains: H, D
    Fragment: FAB
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
    Variant: BALB/CV

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : CDHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FLU2Ligand/Ion2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FLU1Ligand/Ion2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FLU1Ligand/Ion2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:131 , LYS C:188 , ASP C:189 , HOH C:606 , TRP H:33 , TYR H:56 , TYR H:101 , GLY H:102 , TYR H:103 , HOH H:503 , HIS L:31 , ASN L:33 , TYR L:37 , HIS L:39 , TYR L:54 , SER L:96BINDING SITE FOR RESIDUE FLU L 300
2AC2SOFTWAREHIS C:31 , TYR C:37 , HIS C:39 , TYR C:54 , LYS C:55 , SER C:96 , HOH C:668 , TRP D:33 , TYR D:56 , TYR D:101 , GLY D:102 , TYR D:103 , THR L:131 , ASP L:189BINDING SITE FOR RESIDUE FLU C 301

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1C:23 -C:93
2C:139 -C:199
3C:219 -D:220
4D:22 -D:98
5D:145 -D:200
6H:22 -H:98
7H:145 -H:200
8L:23 -L:93
9L:139 -L:199
10L:219 -H:220

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:151 -Pro H:152
5Glu H:153 -Pro H:154
6Trp H:193 -Pro H:194
7Thr C:7 -Pro C:8
8Val C:99 -Pro C:100
9Tyr C:145 -Pro C:146
10Phe D:151 -Pro D:152
11Glu D:153 -Pro D:154
12Trp D:193 -Pro D:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T66)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T66)

(-) Exons   (0, 0)

(no "Exon" information available for 1T66)

(-) 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 C from PDB  Type:PROTEIN  Length:219
 aligned with Q65ZC0_MOUSE | Q65ZC0 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         
         Q65ZC0_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC 219
               SCOP domains d1t66c1 C:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1t66c2 C:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1t66C01 C:1-113 Immunoglobulins                                                                                  1t66C02 C:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeeehhhee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t66 C   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain D from PDB  Type:PROTEIN  Length:220
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:235
                                                                                73 74                                                                                                                                                                                  
                                    29        39        49        59        69   |  | 77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
         Q91Z05_MOUSE    20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSG--STTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCARELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKEC 252
               SCOP domains d1t66d1 D:1-118 Immunoglobulin heavy chain variable domain, VH                                                          d1t66d2 D:119-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                                     SCOP domains
               CATH domains 1t66D01 D:1-118 Immunoglobulins                                                                                         1t66D02 D:119-216 Immunoglobulins                                                                 ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeeee....--eee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...-------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t66 D   1 EVKLDETGGGLVQPGRPMKLSCVASGFTFSDYWMNWVRQSPEKGLEWVAQIRNKPYNYETYYSDSVKGRFTISRDDSKSSVYLQMNNLRAEDMGIYYCTSYGYHG--AYWGQGTLVTVSAAKTTAPSVYPLAPGTAALKSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSALYTLTSSVTVPSSSWPSQTVTCNVAHPASSTKVDKKIVP-------------RNC 220
                                    10        20        30        40        50        60        70        80        90       100    |  108       118       128       138       148       158       168       178       188       198       208        |-         -  |  
                                                                                                                                  105  |                                                                                                            217           218  
                                                                                                                                     106                                                                                                                               


Chain H from PDB  Type:PROTEIN  Length:220
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:235
                                                                                73 74                                                                                                                                                                                  
                                    29        39        49        59        69   |  | 77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
         Q91Z05_MOUSE    20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSG--STTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCARELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKEC 252
               SCOP domains d1t66h1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                          d1t66h2 H:119-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                                     SCOP domains
               CATH domains 1t66H01 H:1-118 Immunoglobulins                                                                                         1t66H02 H:119-216 Immunoglobulins                                                                 ----------------- CATH domains
           Pfam domains (1) V-set-1t66H03 H:1-116                                                                                    --           --------------C1-set-1t66H01 H:131-212                                                          --------------------- Pfam domains (1)
           Pfam domains (2) V-set-1t66H04 H:1-116                                                                                    --           --------------C1-set-1t66H02 H:131-212                                                          --------------------- Pfam domains (2)
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeee....--eee...eeeee........eeeee............eeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeee...........eeeeeehhhheeeeee...-------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t66 H   1 EVKLDETGGGLVQPGRPMKLSCVASGFTFSDYWMNWVRQSPEKGLEWVAQIRNKPYNYETYYSDSVKGRFTISRDDSKSSVYLQMNNLRAEDMGIYYCTSYGYHG--AYWGQGTLVTVSAAKTTAPSVYPLAPGTAALKSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSALYTLTSSVTVPSSSWPSQTVTCNVAHPASSTKVDKKIVP-------------RNC 220
                                    10        20        30        40        50        60        70        80        90       100    |  108       118       128       138       148       158       168       178       188       198       208        |-         -  |  
                                                                                                                                  105  |                                                                                                            217           218  
                                                                                                                                     106                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with Q65ZC0_MOUSE | Q65ZC0 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         
         Q65ZC0_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC 219
               SCOP domains d1t66l1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1t66l2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1t66L01 L:1-113 Immunoglobulins                                                                                  1t66L02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t66 L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    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  (4, 8)

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)
1a1t66C02C:114-216
1b1t66D02D:119-216
1c1t66H02H:119-216
1d1t66C01C:1-113
1e1t66L01L:1-113
1f1t66D01D:1-118
1g1t66H01H:1-118
1h1t66L02L:114-216

(-) 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 1T66)

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  1t66
    Family and Domain Information: ProDom | SYSTERS
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  Q65ZC0_MOUSE | Q65ZC0
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  Q91Z05_MOUSE | Q91Z05
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q65ZC0_MOUSE | Q65ZC0: 2g60
UniProtKB/TrEMBL
        Q65ZC0_MOUSE | Q65ZC0: 1i9i 1i9j 1l7t 1lo2 1lo3 1lo4 2gjz 2gk0
        Q91Z05_MOUSE | Q91Z05: 1i9i 1i9j 1jgu 1jgv 1l7t 1lo2 1lo3 1lo4 2gk0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1T66)