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(-) Description

Title :  FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-L-ALANINE
 
Authors :  B. Golinelli-Pimpaneau, P. Christen
Date :  09 Nov 04  (Deposition) - 30 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  H,L  (1x)
Keywords :  Antibody, Catalytic Antibody, Transamination, Pyridoxal-Phosphate, Phosphopyridoxyl-L-Alanine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Golinelli-Pimpaneau
Structure Of A Pseudomerohedrally Twinned Monoclinic Crystal Form Of A Pyridoxal Phosphate-Dependent Catalytic Antibody
Acta Crystallogr. , Sect. D V. 61 472 2005
PubMed-ID: 15805602  |  Reference-DOI: 10.1107/S0907444905003331
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
    ChainsA, L
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell Line15A9 MURINE HYBRIDOMA
    Expression System StrainBALB/C
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
    ChainsB, H
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell Line15A9 MURINE HYBRIDOMA
    Expression System StrainBALB/C
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABHL
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1IOD5Ligand/IonIODIDE ION
2PP31Ligand/IonALANYL-PYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION
2PP31Ligand/IonALANYL-PYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1IOD3Ligand/IonIODIDE ION
2PP3-1Ligand/IonALANYL-PYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:61 , THR H:68 , ASN H:82ABINDING SITE FOR RESIDUE IOD A1213
2AC2SOFTWAREGLY B:97 , ASN B:100A , TRP B:100EBINDING SITE FOR RESIDUE IOD B1214
3AC3SOFTWAREGLY H:97 , ASN H:100A , TRP H:100EBINDING SITE FOR RESIDUE IOD H1214
4AC4SOFTWARETYR H:33 , ARG H:52 , TYR L:94BINDING SITE FOR RESIDUE IOD H1215
5AC5SOFTWARETHR B:68 , ASN B:82ABINDING SITE FOR RESIDUE IOD L1213
6AC6SOFTWAREASN A:31 , TYR A:32 , HIS A:34 , ARG A:91 , SER A:92 , TYR A:94 , TYR B:33 , ARG B:52 , ASP B:95 , LYS B:96BINDING SITE FOR RESIDUE PP3 A1214

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:195
5H:22 -H:92
6H:140 -H:195
7L:134 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:146 -Pro B:147
5Glu B:148 -Pro B:149
6Arg B:188 -Pro B:189
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149
9Arg H:188 -Pro H:189
10Ser L:7 -Pro L:8
11Tyr L:94 -Pro L:95
12Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WC7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WC7)

(-) Exons   (0, 0)

(no "Exon" information available for 1WC7)

(-) 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 A from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1wc7a1 A:1-107 automated matches                                                                         d1wc7a2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains 1wc7A01 A:1-108 Immunoglobulins                                                                            1wc7A02 A:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeee............eeeee.......ee.....hhhhhhh...ee..eeeee.....eeeeee..eee...ee............eeee.eee.hhhhhh.....eeeee.......eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 A    1 DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
                                                     27|                                                                                                                                                                                         
                                                      29                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1wc7b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wc7b2 B:114-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 --- SCOP domains
               CATH domains 1wc7B01 B:1-113 Immunoglobulins                                                                                              1wc7B02 B:114-214 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....ee.....eee..eee..hhh.eeeeeeee......eeee...hhhhh.....hhhhh..eeeeee....eeeeee...hhhhheeeeeeeeee...............eeeee........eeeee...........eeeeeeee.....eeee........eee...ee....eeeeeee............eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 B    1 EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||     108       118       128|      140       150       160       170       180       190       200       210    
                                                                              52A||                            82A||               100A|||||                         128|                                                                                   
                                                                               52B|                             82B|                100B||||                          131                                                                                   
                                                                                52C                              82C                 100C|||                                                                                                                
                                                                                                                                      100D||                                                                                                                
                                                                                                                                       100E|                                                                                                                
                                                                                                                                        100F                                                                                                                

Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1wc7h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wc7h2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1wc7H01 H:1-113 Immunoglobulins                                                                                              1wc7H02 H:114-212 Immunoglobulins                                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eee..eee..hhh.eeeeeeee......eeeeee.hhhhh..eee.......eeee........eeee...hhhhheeeeeeeeee...............eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 H    1 EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||     108       118       128|      140       150       160       170       180       190       200       210    
                                                                              52A||                            82A||               100A|||||                         128|                                                                                   
                                                                               52B|                             82B|                100B||||                          131                                                                                   
                                                                                52C                              82C                 100C|||                                                                                                                
                                                                                                                                      100D||                                                                                                                
                                                                                                                                       100E|                                                                                                                
                                                                                                                                        100F                                                                                                                

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d1wc7l1 L:1-107 automated matches                                                                         d1wc7l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 1wc7L01 L:1-108 Immunoglobulins                                                                            1wc7L02 L:109-210 Immunoglobulins                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeee............eeeee.......eeeee..hhhhhh....eeeeeee......eeeeeee........ee.................eee.hhhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 L    1 DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
                                                     27|                                                                                                                                                                                        
                                                      29                                                                                                                                                                                        

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1wc7A02A:109-214
1b1wc7L02L:109-210
1c1wc7A01A:1-108
1d1wc7L01L:1-108
1e1wc7B02B:114-214
1f1wc7H02H:114-212
1g1wc7B01B:1-113
1h1wc7H01H:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WC7)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1WC7)

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 Related Entries

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