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(-) Description

Title :  CRYSTAL STRUCTURE OF S25-2 FAB IN COMPLEX WITH KDO ANALOGUES
 
Authors :  C. L. Brooks, S. V. Evans
Date :  23 Aug 07  (Deposition) - 30 Dec 08  (Release) - 30 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fab, Anti-Carbohydrate Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, S. Muller-Loennies, L. Brade, P. Kosma, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
Exploration Of Specificity In Germline Monoclonal Antibody Recognition Of A Range Of Natural And Synthetic Epitopes.
J. Mol. Biol. V. 377 450 2008
PubMed-ID: 18272175  |  Reference-DOI: 10.1016/J.JMB.2008.01.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB, ANTIBODY FRAGMENT (IGG1K), LIGHT CHAIN
    Chains: A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Other Details: ASCITES
 
Molecule 2 - FAB, ANTIBODY FRAGMENT (IGG1K), HEAVY CHAIN
    Chains: B
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Other Details: ASCITES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDD1Ligand/Ion2,6-ANHYDRO-3,5-DIDEOXY-D-RIBO-OCT-2-ENONIC ACID
3MG2Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:32 , SER A:91 , TYR A:92 , ARG A:95 , ARG A:187 , HOH A:261 , TYR B:33 , ARG B:52 , GLU B:100A , HOH B:292 , HOH B:338 , HOH B:339 , HOH B:369BINDING SITE FOR RESIDUE KDA B 212
2AC2SOFTWAREGLU A:184 , HIS A:188 , HOH A:411 , ARG B:52 , THR B:54 , GLU B:56 , HOH B:266BINDING SITE FOR RESIDUE MG B 214
3AC3SOFTWAREGLU A:184 , HIS A:188 , GLU B:56BINDING SITE FOR RESIDUE ZN A 215
4AC4SOFTWAREASN A:137 , HIS B:162BINDING SITE FOR RESIDUE MG A 216
5AC5SOFTWAREARG A:30C , THR A:181 , HOH A:315 , HOH A:371 , HOH A:384BINDING SITE FOR RESIDUE KDD A 217

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:138 -B:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Phe B:144 -Pro B:145
4Glu B:146 -Pro B:147
5Trp B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R1X)

(-) Exons   (0, 0)

(no "Exon" information available for 2R1X)

(-) 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 A from PDB  Type:PROTEIN  Length:219
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  240
               SCOP domains d2r1xa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d2r1xa2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 2r1xA01 A:1-107 Immunoglobulins                                                                                   2r1xA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...-..ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r1x A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYN-LRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103       113       123       133       143       153       163       173       183       193       203       213
                                                        30A|||||                                                             93 |                                                                                                                       
                                                         30B||||                                                               94                                                                                                                       
                                                          30C|||                                                                                                                                                                                        
                                                           30D||                                                                                                                                                                                        
                                                            30E|                                                                                                                                                                                        
                                                             30F                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with A2NU21_MOUSE | A2NU21 from UniProtKB/TrEMBL  Length:119

    Alignment length:215
                                                                                                                              119                                                                                                                  
                                    28        38        48        58        68        78        88        98       108       118|        -         -         -         -         -         -         -         -         -         -         -     
        A2NU21_MOUSE     19 EVKLVESGGGLVQPGGSLSLSCAASGFTFTDYYMSWVRQLPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCAKD------------------------------------------------------------------------------------------------------------------    -
               SCOP domains d2r1xb1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d2r1xb2 B:112-210 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma               SCOP domains
               CATH domains 2r1xB01 B:1-111 Immunoglobulins                                                                                           2r1xB02 B:112-210 Immunoglobulins                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee...............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r1x B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP  210
                                    10        20        30        40        50  ||||| 55        65        75       |84        94      100D|      109       119     ||135       145       155       165       175       185       195       205     
                                                                              52A||||                            82A               100A||||                      125|                                                                              
                                                                               52B|||                                               100B|||                       132                                                                              
                                                                                52C||                                                100C||                                                                                                        
                                                                                 52D|                                                 100D|                                                                                                        
                                                                                  52E                                                  100E
   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, 4)

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 2R1X)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q52L64_MOUSE | Q52L64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain B   (A2NU21_MOUSE | A2NU21)

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  Q52L64_MOUSE | Q52L64
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 Related Entries

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

UniProtKB/TrEMBL
        A2NU21_MOUSE | A2NU21: 2r1w 2r1y 3dur 3dus 3duu 3dv4 3dv6
        Q52L64_MOUSE | Q52L64: 1a3r 1bbd 1h3p 1jgu 1jgv 1q9w 2fd6 2r1w 2r1y 2r23 2r2b 2r2h 3t77

(-) Related Entries Specified in the PDB File

1q9q SAME PROTEIN WITH DIFFERENT LIGAND
2r1w
2r1y
2r23
2r2b
2r2e
2r2h