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(-) Description

Title :  IDENTIFICATION OF KEY RESIDUES OF THE NC6.8 FAB ANTIBODY FRAGMENT BINDING TO SYNTHETIC SWEETERNERS: CRYSTAL STRUCTURE OF NC6.8 CO-CRYSTALIZED WITH HIGH POTENCY SWEETENER COMPOUND SC45647
 
Authors :  K. Gokulan, S. Khare, D. R. Ronning, S. D. Linthicum, J. C. Sacchettini,
Date :  24 Jan 05  (Deposition) - 16 Aug 05  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Triethyl Aminomethane Sulfonyl Acid, Sweetener Compound, Sc45647 And Nc174, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, S. Khare, D. R. Ronning, S. D. Linthicum, J. C. Sacchettini B. Rupp
Cocrystal Structures Of Nc6. 8 Fab Identify Key Interactions For High Potency Sweetener Recognition: Implications For Th Design Of Synthetic Sweeteners
Biochemistry V. 44 9889 2005
PubMed-ID: 16026161  |  Reference-DOI: 10.1021/BI050613U

(-) Compounds

Molecule 1 - IG GAMMA LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MONOCLONAL ANTIBODY FAB FRAGMENT
 
Molecule 2 - IG GAMMA HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NES1Ligand/Ion2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:96 , SER H:97 , SER H:98 , HIS L:27D , TYR L:32 , HIS L:34 , GLY L:91 , THR L:92 , TYR L:96 , HOH L:543 , HOH L:693 , HOH L:694 , HOH L:695 , HOH L:696BINDING SITE FOR RESIDUE NES L 501

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:139 -H:194
3L:23 -L:88
4L:134 -L:194
5L:214 -H:127

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:145 -Pro H:146
5Ser H:160 -Ser H:161
6Trp H:187 -Pro H:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YNL)

(-) 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:219
 aligned with Q6PJB2_MOUSE | Q6PJB2 from UniProtKB/TrEMBL  Length:465

    Alignment length:219
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229         
         Q6PJB2_MOUSE    20 QVQLKQSGAELVKPGASVKLSCKASGYTFNSYIMHWVKQRPGQGLEWIGYFSPYNDDTKCNEKFKGKATLTADKSSSTAYMELSSLTSEDSAVYYCARGYYVFDYWGQGTTITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT 238
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ynlH01 H:1-112 Immunoglobulins                                                                                     1ynlH02 H:113-215 Immunoglobulins                                                                       CATH domains
               Pfam domains -V-set-1ynlH02 H:2-110                                                                                            --------------C1-set-1ynlH01 H:125-206                                                          --------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ynl H   1 RVQLLESGAELMKPGASVQISCKATGYTFSFYWIEWVKERPGHGLEWIGEILPGSGRTNYREKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCTRGYSSMDYWGQGTSVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPI 215
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206         
                                                                              52A                            82A||                                                                                                                                     
                                                                                                              82B|                                                                                                                                     
                                                                                                               82C                                                                                                                                     


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2P1G9_MOUSE | A2P1G9 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         
         A2P1G9_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQVTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC 219
               SCOP domains d1ynll1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1ynll2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ynlL01 L:1-108 Immunoglobulins                                                                                  1ynlL02 L:109-211 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
                 1ynl L   1 ELVMTQSPLSLPVSLGDQASISCRPSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTAFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    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
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q6PJB2_MOUSE | Q6PJB2)

Chain L   (A2P1G9_MOUSE | A2P1G9)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A2P1G9_MOUSE | A2P1G9: 4zxb
        IGG2B_MOUSE | P01867: 1cbv 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ztx 2gjz 2gk0 2q8a 2q8b 2rgs 3cfd 3cfe
UniProtKB/TrEMBL
        A2P1G9_MOUSE | A2P1G9: 1cgs 1ynk 2cgr
        Q6PJB2_MOUSE | Q6PJB2: 1ynk 2r6p

(-) Related Entries Specified in the PDB File

1ynk