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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TEPC15-VK45.1 ANTI-2-PHENYL-5-OXAZOLONE NQ16-113.8 SCFV IN COMPLEX WITH PHOXGABA
 
Authors :  C. Scotti, E. Gherardi
Date :  09 Apr 06  (Deposition) - 20 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Scfv, Antibody, Immunoglobulin, 2-Phenyl-5-Oxazolone, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Scotti, E. Gherardi
Structural Basis Of Affinity Maturation Of The Tepc15/V(Kappa)45. 1 Anti-2-Phenyl-5-Oxazolone Antibodies.
J. Mol. Biol. V. 359 1161 2006
PubMed-ID: 16682055  |  Reference-DOI: 10.1016/J.JMB.2006.04.036

(-) Compounds

Molecule 1 - NQ16-113.8 ANTI-PHOX ANTIBODY
    Cell: HYBRIDOMA
    Chains: H
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9KE
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA
    Strain: BALB/C
 
Molecule 2 - NQ16-113.8 ANTI-PHOX ANTIBODY
    Cell: HYBRIDOMA
    Chains: L
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9KE
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA
    Strain: BALB/C

 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
1PHX1Ligand/Ion4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:31 , TYR H:32 , TYR H:33 , ASN H:52A , GLY H:95 , TYR H:96 , GLY H:97 , ALA H:100 , TRP H:100A , HOH H:2011 , HOH H:2013 , TYR L:32 , ARG L:54BINDING SITE FOR RESIDUE PHX H1114

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CJU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CJU)

(-) 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:121
 aligned with HVM20_MOUSE | P01789 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:123
                                                                                                                                 103                   
                                                                                                                               102 |                   
                                    10        20        30        40        50        60        70        80        90       100 | |   109       119   
         HVM20_MOUSE      1 EVKLVESGGGLVQPGGSLRLSCATSGFTFSDFYMEWVRQPPGKRLEWIAASRNKGNKYTTEYSASVKGRFIVSRDTSQSILYLQMNALRAEDTAIYYCARNY-YGSTWYFDVWGAGTTVTVSS  122
               SCOP domains d2cjuh_ H: automated matches                                                                                                SCOP domains
               CATH domains 2cjuH00 H:1-113 Immunoglobulins                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee...-ee-eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                2cju H    1 EVKLVESGGGLVQPGGSLRLSCATSGFTFTNYYMNWVRQPPGKALEWLVSIRNKANGYTTDYSASVKGRFTISRDNSQSILYLEMNNLRAEDSATYYCARGYGYG-AW-FAYWGQGTLVTVSA  113
                                    10        20        30        40        50  |||   57        67        77     |||84        94    | 100B       110   
                                                                              52A||                            82A||               99 || |             
                                                                               52B|                             82B|                100| |             
                                                                                52C                              82C                100A |             
                                                                                                                                      100B             


Chain L from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d2cjul_ L: automated matches                                                                                      SCOP domains
               CATH domains 2cjuL00 L:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2cju L    1 QVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKR  107
                                    10        20       27C||      35        45        55        65        75        85        95       105 | 
                                                     27A||||                                                                            106A 
                                                      27B|||                                                                                 
                                                       27C||                                                                                 
                                                        27D|                                                                                 
                                                         27E
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CJU)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM20_MOUSE | P01789)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM20_MOUSE | P01789: 1mcp 2mcp

(-) Related Entries Specified in the PDB File

2cjv CRYSTAL STRUCTURE OF THE TEPC15-VK45.1 ANTI-2-PHENYL-5-OXAZOLONE NQ10-1.12 SCFV IN COMPLEX WITH PHOXGABA