Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)GLN 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 :  2.18
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 , SER H:169 , HOH H:234 , HIS L:31 , PHE L:94 , GLY L:96 , SER L:97 , LEU L:99 , HOH L:223BINDING SITE FOR RESIDUE BZH H 401
2AC2SOFTWAREHIS A:31 , PHE A:94 , GLY A:96 , SER A:97 , LEU A:99 , HOH A:237 , HOH A:243 , ASP B:35 , TRP B:52 , HIS B:98 , PRO B:105 , MET B:108BINDING SITE FOR RESIDUE BZH A 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 3FO2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FO2)

(-) Exons   (0, 0)

(no "Exon" information available for 3FO2)

(-) 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 d3fo2a1 A:1-112 automated matches                                                                               d3fo2a2 A:113-216 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo2A02 A:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fo2 A   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLQWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 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 3fo2B01 B:1-120 Immunoglobulins                                                                                         ---3fo2B02 B:124-221 Immunoglobulins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeee.......eeeee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo2 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fo2H01 H:1-120 Immunoglobulins                                                                                         ---3fo2H02 H:124-221 Immunoglobulins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.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
                 3fo2 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 d3fo2l1 L:1-112 automated matches                                                                               d3fo2l2 L:113-216 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo2L02 L:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...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
                 3fo2 L   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLQWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 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 3FO2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FO2)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BZH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:156 - Pro B:157   [ RasMol ]  
    Glu H:156 - Pro H:157   [ RasMol ]  
    Leu A:99 - Pro A:100   [ RasMol ]  
    Leu L:99 - Pro L:100   [ RasMol ]  
    Phe B:154 - Pro B:155   [ RasMol ]  
    Phe H:154 - Pro H:155   [ RasMol ]  
    Thr A:7 - Pro A:8   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Tyr A:145 - Pro A:146   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3fo2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3FO2)

(-) 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)
3fo1 HAPTEN COMPLEX OF CATALYTIC ELIMINATION ANTIBODY 13G5 (GLU(L39)ALA MUTANT)