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

(-) Description

Title :  DECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX
 
Authors :  K. Hotta, I. A. Wilson
Date :  09 Nov 99  (Deposition) - 11 Oct 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Catalytic Antibody, Chimeric Fab, Decarboxylase, Hapten Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Hotta, H. Lange, D. J. Tantillo, K. N. Houk, D. Hilvert, I. A. Wilson
Catalysis Of Decarboxylation By A Preorganized Heterogeneou Microenvironment: Crystal Structures Of Abzyme 21D8.
J. Mol. Biol. V. 302 1213 2000
PubMed-ID: 11183784  |  Reference-DOI: 10.1006/JMBI.2000.4503

(-) Compounds

Molecule 1 - CHIMERIC DECARBOXYLASE ANTIBODY 21D8
    CellB-LYMPHOCYTE
    Cell Line21D8
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationPERIPLASM
    Expression System PlasmidP4XH-M13
    Expression System StrainTOPP2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFAB
    OrganSPLEEN
    Organism CommonHOUSE MOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090,9606
    Other DetailsTHE CONSTANT DOMAIN (RESIDUES 103-214) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-102) IS FROM MURINE SOURCE
    StrainBALB/C, BALB/C
 
Molecule 2 - CHIMERIC DECARBOXYLASE ANTIBODY 21D8
    CellB-LYMPHOCYTE
    Cell Line21D8
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationPERIPLASM
    Expression System PlasmidP4XH-M13
    Expression System StrainTOPP2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFAB
    OrganSPLEEN
    Organism CommonHOUSE MOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090,9606
    Other DetailsTHE CONSTANT DOMAIN (RESIDUES 109-230) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-108) IS FROM MURINE SOURCE
    StrainBALB/C, BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TK41Ligand/Ion2-ACETYLAMINO-NAPTHALENE-1,5-DISULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , HIS H:35 , ILE H:95 , ALA H:101 , TRP H:103 , SER L:34 , LEU L:36 , ARG L:46 , SER L:67 , ASP L:70 , LEU L:89 , TYR L:91 , ARG L:96 , HOH L:1064 , HOH L:1089BINDING SITE FOR RESIDUE TK4 L 1001
2AC2SOFTWAREPHE H:174 , PRO H:175 , VAL H:177 , SER H:186 , LEU H:187 , SER H:188 , HOH H:2027 , GLN L:160 , SER L:162 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL H 2001
3AC3SOFTWARETHR H:9 , LEU H:11 , LEU H:108 , GLU H:150 , HOH H:2016 , HOH H:2135 , HOH L:1014 , HOH L:1052BINDING SITE FOR RESIDUE GOL H 2002

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C5C)

(-) Exons   (0, 0)

(no "Exon" information available for 1C5C)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains d1c5ch1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                  d1c5ch2 H:114-230 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1c5cH01 H:1-113 Immunoglobulins                                                                                 1c5cH02 H:114-227 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee....hhh.eeeeeee..ee...eeeee.......................................eeee...............................hhhhh....eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5c H   1 QVQLLEPGTELVKPGASVKLSCRASGYSFTSYWMHWVKQRPGQGLEWIGLIDPSNGRTNFNDKFKSRATLTVDTSSSTAYMQLSSLTSEDSAVYYCVRIAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 230
                                    10        20        30        40        50  |     59        69        79   |||  86       101       111       121       133       143       153||||   168||     179||     190       200||     213       223|    
                                                                              52A                            82A||           95|                          130|                  154|||    169|      180|               200||               223|    
                                                                                                              82B|           101                           133                   156||     171       182                203|                226    
                                                                                                               82C                                                                157|                                   205                       
                                                                                                                                                                                   162                                                             

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1c5cl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1c5cl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1c5cL01 L:1-108 Immunoglobulins                                                                             1c5cL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee....hhh..eeeeee......ee...eeeee.......eeeee...hhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5c L   1 EIQLTQSPSSLSASLGERVSLTCRTSQEISGYLSWLQQKPDGTIKRLIYDATKLDSGAPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYASFPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C5C)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1C5C)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TK4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Phe L:94 - Pro L:95   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1c5c
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB 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 ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1C5C)

(-) Related Entries Specified in the PDB File

1c5b DECARBOXYLASE CATALYTIC ANTIBODY 21D8 UNLIGANDED