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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE HYDROLYTIC ANTIBODY FAB 6D9 AND A TRANSITION-STATE ANALOG
 
Authors :  O. Kristensen, D. G. Vassylyev, F. Tanaka, N. Ito, K. Morikawa, I. Fujii
Date :  30 May 06  (Deposition) - 20 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Catalytic Antibody, Ester Hydrolysis, Esterolytic, Fab, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Oda, N. Ito, T. Tsumuraya, K. Suzuki, M. Sakakura, I. Fujii
Thermodynamic And Structural Basis For Transition-State Stabilization In Antibody-Catalyzed Hydrolysis
J. Mol. Biol. V. 369 198 2007
PubMed-ID: 17428500  |  Reference-DOI: 10.1016/J.JMB.2007.03.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN 6D9
    Cell Line: 6D9 MURINE-MURINE HYBRIDOMA
    Chains: L
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Secretion: ASCITES FLUID
    Synonym: CATALYTIC ANTIBODY 6D9
 
Molecule 2 - IMMUNOGLOBULIN 6D9
    Cell Line: 6D9 MURINE-MURINE HYBRIDOMA
    Chains: H
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Secretion: ASCITES FLUID
    Synonym: CATALYTIC ANTIBODY 6D9

 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
1CPD1Ligand/Ion[1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA H:33 , SER H:50 , SER H:52 , TYR H:58 , VAL H:95 , HIS H:97 , ASP H:99 , GLY H:100 , TRP H:100I , PHE H:100K , ASP H:214 , HIS L:27D , PHE L:89 , GLY L:91 , VAL L:94 , GLU L:213 , CYS L:214BINDING SITE FOR RESIDUE CPD H 501

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194
5L:214 -H:215

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DQT)

(-) 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:218
 aligned with HVM56_MOUSE | P18527 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:218
                                                                                                                          97                                                                                                                          
                                    11        21        31        41        51        61        71        81        91     |   -         -         -         -         -         -         -         -         -         -         -         -        
         HVM56_MOUSE      2 VKLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVASISSGGSTYYPDSVKGRFTISRDNARNILYLQMSSLRSEDTAMYYCAR--------------------------------------------------------------------------------------------------------------------------    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------d2dqth1 H:114-215 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 2dqtH01 H:2-113 Immunoglobulins                                                                                          2dqtH02 H:114-212 Immunoglobulins                                                             --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dqt H    2 VKLVESGGGLVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVVSISSGGSIYYLDSVKGRFTVSRDNARNILYLQMTSLRSEDTAMYFCARVSHYDGSRDWYFDVWGAGTSVTVSSAKTTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  215
                                    11        21        31        41        51 | ||   61        71        81 |||    88        98  |||||102       112       122    || 137       147       157       167       177       187       197       207        
                                                                             52A ||                        82A||               100A|||||                        127|                                                                                  
                                                                                54|                         82B|                100B||||                         133                                                                                  
                                                                                 56                          82C                 100C|||                                                                                                              
                                                                                                                                  100I||                                                                                                              
                                                                                                                                   100J|                                                                                                              
                                                                                                                                    100K                                                                                                              


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 d2dqtl1 L:1-107 automated matches                                                                               d2dqtl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 2dqtL01 L:1-108 Immunoglobulins                                                                                  2dqtL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dqt L    1 DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGDTYLDWFLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  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)
  - → 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  (3, 3)

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 2DQT)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM56_MOUSE | P18527)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain L   (A2NHM3_MOUSE | A2NHM3)

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  2dqt
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  HVM56_MOUSE | P18527
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        HVM56_MOUSE | P18527: 1ub5 1ub6 2dqu 2dtm 3ab0
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

2dqu THE SAME PROTEIN(CRYSTAL FORM II)