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 :  STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE
 
Authors :  B. Gigant, M. Knossow
Date :  29 May 97  (Deposition) - 03 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Catalytic Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gigant, J. B. Charbonnier, Z. Eshhar, B. S. Green, M. Knossow
X-Ray Structures Of A Hydrolytic Antibody And Of Complexes Elucidate Catalytic Pathway From Substrate Binding And Transition State Stabilization Through Water Attack And Product Release.
Proc. Natl. Acad. Sci. Usa V. 94 7857 1997
PubMed-ID: 9223277  |  Reference-DOI: 10.1073/PNAS.94.15.7857
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2A FAB FRAGMENT
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3)
 
Molecule 2 - IGG2A FAB FRAGMENT
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1PNC1Ligand/IonPARA-NITROBENZYL GLUTARYL GLYCINIC ACID
2ZN8Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREZN L:219 , ZN L:221 , HOH L:574 , HOH L:604 , HOH L:605 , HOH L:637 , HOH L:645BINDING SITE FOR RESIDUE ZN L 215
2AC2SOFTWAREZN L:218 , PNC L:551 , HOH L:555 , HOH L:556 , HOH L:589BINDING SITE FOR RESIDUE ZN L 216
3AC3SOFTWAREASP H:100C , HIS L:49 , HOH L:592 , HOH L:597BINDING SITE FOR RESIDUE ZN L 217
4AC4SOFTWAREASP H:181 , HIS L:93 , ZN L:216 , ZN L:222 , HOH L:589 , HOH L:642BINDING SITE FOR RESIDUE ZN L 218
5AC5SOFTWAREASP L:151 , HIS L:189 , ZN L:215 , ZN L:220 , HOH L:587 , HOH L:604 , HOH L:645BINDING SITE FOR RESIDUE ZN L 219
6AC6SOFTWAREZN L:219 , ZN L:221 , HOH L:587 , HOH L:606 , HOH L:615 , HOH L:645BINDING SITE FOR RESIDUE ZN L 220
7AC7SOFTWAREASP L:60 , ZN L:215 , ZN L:220 , HOH L:605 , HOH L:606 , HOH L:608 , HOH L:625 , HOH L:645BINDING SITE FOR RESIDUE ZN L 221
8AC8SOFTWARESER H:112 , ZN L:218 , HOH L:621 , HOH L:642BINDING SITE FOR RESIDUE ZN L 222
9AC9SOFTWAREHIS H:35 , VAL H:37 , THR H:93 , TRP H:95 , TYR H:100D , TRP H:103 , HOH H:224 , TYR L:27D , VAL L:89 , GLY L:91 , THR L:92 , TYR L:96 , PHE L:98 , ZN L:216 , HOH L:555 , HOH L:557BINDING SITE FOR RESIDUE PNC L 551

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:206
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

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:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:197 -Pro H:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YEF)

(-) 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:222
                                                                                                                                                                                                                                                               
               SCOP domains d1yefh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1yefh2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1yefH01 H:1-113 Immunoglobulins                                                                                            1yefH02 H:114-223 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeee...................eeeee........eeeee..........eeeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1yef H    1 EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  223
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130       140       150 ||||  165 ||    176 ||    188     ||200   ||  211       221  
                                                                              52A                            82A||               100A|||||                                                 152|||    167|      178|          194| || 204|                 
                                                                                                              82B|                100B||||                                                  154||     169       181           196 ||  206                 
                                                                                                               82C                 100C|||                                                   155|                               198|                      
                                                                                                                                    100D||                                                    160                                200                      
                                                                                                                                     100E|                                                                                                                
                                                                                                                                      100F                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1yefl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yefl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yefL01 L:1-108 Immunoglobulins                                                                                  1yefL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeee......eeeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yef L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRGDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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 1YEF)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    PNC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe L:94 - Pro L:95   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:197 - Pro H:198   [ 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
[ 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
  1yef
    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
  GCAA_MOUSE | P01863
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  GCAA_MOUSE | P01863
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yec 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YEF)