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(-) Description

Title :  CRYSTAL STRUCTURE OF HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (WILD-TYPE)
 
Authors :  E. W. Debler, I. A. Wilson
Date :  27 Dec 08  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Catalytic Antibody, Chimeric Fab, Hapten Complex, Acid Base Catalysis, Proton Transfer, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Debler, R. Muller, D. Hilvert, I. A. Wilson
An Aspartate And A Water Molecule Mediate Efficient Acid-Base Catalysis In A Tailored Antibody Pocket.
Proc. Natl. Acad. Sci. Usa V. 106 18539 2009
PubMed-ID: 19846764  |  Reference-DOI: 10.1073/PNAS.0902700106

(-) Compounds

Molecule 1 - CATALYTIC ANTIBODY FAB 13G5 KAPPA LIGHT CHAIN CHIMERA
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P4XH-M13
    Expression System Strain: TOPP2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: FUSION PROTEIN. THE VARIABLE DOMAIN (RESIDUES 1-107) IS FROM A MURINE SOURCE AND THE CONSTANT DOMAIN (RESIDUES 108-214) IS FROM A HUMAN SOURCE
 
Molecule 2 - CATALYTIC ANTIBODY FAB 13G5 IGG2B HEAVY CHAIN CHIMERA
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P4XH-M13
    Expression System Strain: TOPP2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: FUSION PROTEIN. THE VARIABLE DOMAIN (RESIDUES 1-113) IS FROM A MURINE SOURCE AND THE CONSTANT DOMAIN (RESIDUES 114-235) IS FROM A HUMAN SOURCE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BZH1Ligand/Ion5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOICACID
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:35 , TRP H:52 , HIS H:98 , PRO H:105 , MET H:108 , SER H:169 , HIS L:31 , PHE L:94 , GLY L:96 , SER L:97 , LEU L:99 , PRO L:101 , HOH L:226 , HOH L:243BINDING SITE FOR RESIDUE BZH H 401
2AC2SOFTWARETYR H:32 , GLY H:33 , HIS H:98 , GLY H:100 , GLY H:101 , TYR H:102 , PRO H:105 , HOH H:240BINDING SITE FOR RESIDUE GOL H 501

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2H:148 -H:204
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Leu L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:154 -Pro H:155
5Glu H:156 -Pro H:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FO0)

(-) Exons   (0, 0)

(no "Exon" information available for 3FO0)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fo0H01 H:1-120 Immunoglobulins                                                                                         ---3fo0H02 H:124-221 Immunoglobulins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee.......eeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo0 H   1 DVQLLESGPGLVAPSQSLSITCTVSGFSLTNYGVDWVRQPPGKGLEWVGVIWSGGSTNYNSALMSRLSISKDNSKSQVFLKMNSLQTDDTAVYYCAKHWGGYYIPYGMDHWGQGTTVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  147       157       167       177       187       197       207       217    
                                                                                                                                                               134|                                                                               
                                                                                                                                                                142                                                                               


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3fo0l1 L:1-112 automated matches                                                                               d3fo0l2 L:113-216 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo0L02 L:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fo0 L   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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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  (2, 2)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FO0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FO0)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3FO0)

(-) Related Entries Specified in the PDB File

2gjz CATALYTIC ELIMINATION ANTIBODY 13G5 FROM A CRYSTAL IN SPACE GROUP P2(1)
2gk0 CATALYTIC ELIMINATION ANTIBODY 13G5 FROM A TWINNED CRYSTAL IN SPACE GROUP C2
3fo1 HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)ALA MUTANT)
3fo2 HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)GLN MUTANT)