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(-) Description

Title :  CRYSTAL STRUCTURE OF HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)ALA MUTANT)
 
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 :  2.20
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B,H,L  (1x)
Biol. Unit 2:  A,B,H,L  (1x)
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, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P4XH-M13
    Expression System Strain: TOPP2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    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, B
    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

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x): ABHL
Biological Unit 2 (1x): ABHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BZH2Ligand/Ion5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOICACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BZH2Ligand/Ion5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOICACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BZH2Ligand/Ion5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:35 , TRP H:52 , HIS H:98 , PRO H:105 , MET H:108 , HIS L:31 , PHE L:94 , GLY L:96 , SER L:97 , LEU L:99BINDING SITE FOR RESIDUE BZH H 401
2AC2SOFTWAREHIS A:31 , PHE A:94 , GLY A:96 , SER A:97 , LEU A:99 , PRO A:101 , ASP B:35 , TRP B:52 , HIS B:98 , ILE B:104 , PRO B:105 , MET B:108 , HOH B:238BINDING SITE FOR RESIDUE BZH B 401

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:93
2A:139 -A:199
3B:22 -B:95
4B:148 -B:204
5H:22 -H:95
6H:148 -H:204
7L:23 -L:93
8L:139 -L:199

(-) Cis Peptide Bonds  (10, 10)

Asymmetric 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
6Thr A:7 -Pro A:8
7Leu A:99 -Pro A:100
8Tyr A:145 -Pro A:146
9Phe B:154 -Pro B:155
10Glu B:156 -Pro B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FO1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FO1)

(-) Exons   (0, 0)

(no "Exon" information available for 3FO1)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d3fo1a1 A:1-112 automated matches                                                                               d3fo1a2 A:113-216 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo1A02 A: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........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fo1 A   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLAWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fo1B01 B:1-120 Immunoglobulins                                                                                         ---3fo1B02 B:124-221 Immunoglobulins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee.......eeeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo1 B   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 H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3fo1H01 H:1-120 Immunoglobulins                                                                                         ---3fo1H02 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.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fo1 H   1 DVQLLESGPGLVAPSQSLSITCTVSGFSLTNYGVDWVRQPPGKGLEWVGVIWSGGSTNYNSALMSRLSISKDNSKSQVFLKMNSLQTDDTAVYYCAKHWGGYYIPYGMDHWGQGTTVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215      
                                                                                                                                                               134|                                                                                 
                                                                                                                                                                140                                                                                 


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3fo1l1 L:1-112 automated matches                                                                               d3fo1l2 L:113-216 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo1L02 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.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fo1 L   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLAWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FO1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FO1)

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 Related Entries

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

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(-) 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
3fo0 HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (WILD -TYPE)
3fo2 HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)GLN MUTANT)