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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TEPC15-VK45.1 ANTI-2-PHENYL-5-OXAZOLONE NQ10-1.12 SCFV IN COMPLEX WITH THE HAPTEN
 
Authors :  C. Scotti, E. Gherardi
Date :  02 Mar 07  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  H,J,K,L,S,T
Biol. Unit 1:  H,L,S  (1x)
Biol. Unit 2:  J,K,T  (1x)
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-Vkappa45. 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 - NQ10-1.12 ANTI-PHOX ANTIBODY
    Cell: HYBRIDOMA
    Chains: H, J
    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: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA
    Strain: BALB/C
 
Molecule 2 - NQ10-1.12 ANTI-PHOX ANTIBODY
    Cell: HYBRIDOMA
    Chains: S, T
    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: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA
    Strain: BALB/C
 
Molecule 3 - NQ10-1.12 ANTI-PHOX ANTIBODY
    Cell: HYBRIDOMA
    Chains: K, 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: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HJKLST
Biological Unit 1 (1x): H  LS 
Biological Unit 2 (1x):  JK  T

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PHX2Ligand/Ion4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PHX1Ligand/Ion4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PHX1Ligand/Ion4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:31 , TYR H:32 , TYR H:33 , ASP H:96 , TYR H:97 , TYR H:98 , ALA H:100 , TRP H:100A , HOH H:2024 , ARG K:54BINDING SITE FOR RESIDUE PHX H1114
2AC2SOFTWAREASP J:31 , TYR J:32 , TYR J:33 , GLY J:95 , ASP J:96 , TYR J:97 , ALA J:100 , TRP J:100A , ARG L:54 , ASP L:60BINDING SITE FOR RESIDUE PHX J1114

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1H:22 -H:92
2J:22 -J:92
3L:23 -L:88

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val K:94 -Pro K:95
2Thr L:7 -Pro L:8
3Val L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UUD)

(-) 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 H from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains d2uudh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                            SCOP domains
               CATH domains 2uudH00 H:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.hhhh...eeeee....eeeeee...hhhhheeeeeeeee...eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                2uud H    1 EVKLVESGGGLVQPGGSLRLSCATSGFSFTDYYMAWVRQPPGKALEWLAFIRNKANGYTTDYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARGDYYGAWFAYWGQGTLVTVSA  113
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |102       112 
                                                                              52A||                            82A||               100A|             
                                                                               52B|                             82B|                100B             
                                                                                52C                              82C                                 


Chain J from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains d2uudj1 J:1-113 Immunoglobulin heavy chain variable domain, VH                                                            SCOP domains
               CATH domains 2uudJ00 J:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee......eeeeeee..hhhhh.eeeeee......eeeeee.hhhhh............eeeee.....eeeeee...hhhhheeeeeee.........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                2uud J    1 EVKLVESGGGLVQPGGSLRLSCATSGFSFTDYYMAWVRQPPGKALEWLAFIRNKANGYTTDYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARGDYYGAWFAYWGQGTLVTVSA  113
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |102       112 
                                                                              52A||                            82A||               100A|             
                                                                               52B|                             82B|                100B             
                                                                                52C                              82C                                 


Chain K from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d2uudk_ K: automated matches                                                                                      SCOP domains
               CATH domains 2uudK00 K:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.......eeeee.............eeeeee......ee.................eeee..eeeee.........eeeeeee......ee...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2uud K    1 QVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKR  107
                                    10        20       27C||      35        45        55        65        75        85        95       105 | 
                                                     27A||||                                                                            106A 
                                                      27B|||                                                                                 
                                                       27C||                                                                                 
                                                        27D|                                                                                 
                                                         27E                                                                                 


Chain L from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d2uudl_ L: automated matches                                                                                      SCOP domains
               CATH domains 2uudL00 L:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...........eeeeee.............eeeeee......ee...............eeee....eeeeee...hhhhh.eeeeee......ee...ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2uud L    1 QVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKR  107
                                    10        20       27C||      35        45        55        65        75        85        95       105 | 
                                                     27A||||                                                                            106A 
                                                      27B|||                                                                                 
                                                       27C||                                                                                 
                                                        27D|                                                                                 
                                                         27E                                                                                 


Chain S from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                2uud S    1 STSSGGGSA   18
                                ||   
                                5|   
                                15   


Chain T from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                2uud T    1 STSGGSGGSA   18
                              ||    18
                              3|      
                              12
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2UUD)

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(-) Related Entries Specified in the PDB File

2cju CRYSTAL STRUCTURE OF THE TEPC15-VK45.1 ANTI-2-PHENYL-5-OXAZOLONE NQ16-113.8 SCFV IN COMPLEX WITH PHOXGABA
2dlf HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75