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 :  CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393 AND A TRANSITION-STATE ANALOG
 
Authors :  S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J Y. Nishi, D. W. Rice
Date :  27 Aug 02  (Deposition) - 23 Sep 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Catalytic Antibody, Ester Hydrolysis, Esterolytic, Fab, Immunoglobulin, Tsa, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J. Sun, Y. Nishi, D. W. Rice
High-Resolution Crystal Structure Of The Fab-Fragments Of A Family Of Mouse Catalytic Antibodies With Esterase Activity
J. Mol. Biol. V. 332 423 2003
PubMed-ID: 12948492  |  Reference-DOI: 10.1016/S0022-2836(03)00902-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN MS5-393
    Cell Line: HYBRIDOMA
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT, LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL
 
Molecule 2 - IMMUNOGLOBULIN MS5-393
    Cell Line: HYBRIDOMA
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT, HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HAL1Ligand/IonN-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , ASN H:35 , ASN H:50 , VAL H:93 , LYS H:95 , TRP H:103 , TYR L:32 , HIS L:91 , LEU L:92 , TYR L:94 , PHE L:96BINDING SITE FOR RESIDUE HAL H 301

(-) 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
1Tyr L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 1MJ7)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains d1mj7h1 H:4-113 Immunoglobulin heavy chain variable domain, VH                                      d1mj7h2 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma               SCOP domains
               CATH domains 1mj7H01 H:4-113 Immunoglobulins                                                                     1mj7H02 H:114-222 Immunoglobulins                                                        ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee...eeeeeee......eeeeee...eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj7 H   4 LQQPGAELVKPGASVKLSCSSWINWVKQRPGQGLEWIGNVYPSTNYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAFYYCVRKDFPYWGQGTLVTVSAAKTTAPSVYPLAPSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    13        31        41        51 ||     63        73       82A||      90     ||103       113       123  ||   142       152 ||||  167 ||    178 ||    190     ||202   ||  213       223|  
                                             22|                   52A|                        82A||            96|                       126|               154|||    169|      180|          196| || 206|            223|  
                                              31                     56                         82B|            100                        136                157||     171       183           198 ||  208             226  
                                                                                                 82C                                                           158|                               200|                       
                                                                                                                                                                162                                202                       


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1mj7l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mj7l2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1mj7L01 L:1-108 Immunoglobulins                                                                                  1mj7L02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj7 L   1 EIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLNWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSETAFTLRTSRVEAEDVGVYYCMQHLEYPFTFGSGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MJ7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1MJ7)

 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
    HAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Trp H:199 - Pro H:200   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1mj7
    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 1MJ7)

(-) Related Entries Specified in the PDB File

1mh5 THE STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THEESTEROLYTIC ANTIBODY MS6-164 AND A TRANSITION-STATE ANALOG
1mie CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393
1mj8 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THE ESTEROLYTIC ANTIBODY MS6-126 AND A TRANSITION-STATE ANALOG
1mjj HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION- STATE ANALOG
1mju 1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12