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 :  LOCAL AND TRANSMITTED CONFORMATIONAL CHANGES ON COMPLEXATION OF AN ANTI-SWEETENER FAB
 
Authors :  L. W. Guddat, L. Shan, A. B. Edmundson
Date :  23 Nov 93  (Deposition) - 31 May 94  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Guddat, L. Shan, J. M. Anchin, D. S. Linthicum, A. B. Edmundson
Local And Transmitted Conformational Changes On Complexation Of An Anti-Sweetener Fab.
J. Mol. Biol. V. 236 247 1994
PubMed-ID: 7893280  |  Reference-DOI: 10.1006/JMBI.1994.1133
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2B-KAPPA NC6.8 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG2B-KAPPA NC6.8 FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 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
1GAS1Ligand/IonN-(P-CYANOPHENYL)-N'-DIPHENYLMETHYL-GUANIDINE-ACETICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , GLU H:35 , GLU H:50 , ARG H:57 , ASN H:59 , TYR H:100 , SER H:101 , HIS L:31 , TYR L:37 , HIS L:39 , GLY L:96 , TYR L:101 , HOH L:268BINDING SITE FOR RESIDUE GAS H 215
2LHSAUTHORHIS L:31 , TYR L:37 , HIS L:39 , GLY L:96 , TYR L:101 , TRP H:33 , GLU H:35 , GLU H:50 , ARG H:57 , ASN H:59 , TYR H:100 , SER H:101 , SER H:102HAPTEN BINDING SITE

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:143 -H:198
3L:23 -L:93
4L:139 -L:199
5L:219 -H:131

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:149 -Pro H:150
5Trp H:191 -Pro H:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CGR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CGR)

(-) Exons   (0, 0)

(no "Exon" information available for 2CGR)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains d2cgrh1 H:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d2cgrh2 H:118-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 2cgrH01 H:1-116 Immunoglobulins                                                                                     2cgrH02 H:117-214 Immunoglobulins                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eee....eee.....eeeeeeee.......eeeeeeee..eeeeeeeeee....eeeee.....------hhhhh-------.......eeeeeeee.....eeeeeeeeeee.......eeeee...........eeeeeeeeee.....eeeeeee....eeeeeeeeee..eeeeeeeeee...hhhhheeeeeeee....eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------eeeeeee---eeeeeeee---------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cgr H   1 RVQLLESGAELMKPGASVQISCKATGYTFSEYWIEWVKERPGHGLEWIGEILPGSGRTNYREKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCTRGYSSMDYWGQGTSVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLE 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2P1G9_MOUSE | A2P1G9 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
         A2P1G9_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQVTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC 219
               SCOP domains d2cgrl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d2cgrl2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2cgrL01 L:1-113 Immunoglobulins                                                                                  2cgrL02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeee.eeeee.....eeeeeeee..........eeeeeeee..eeeeeeeee..eee.......eeeee..eeeeee........eeeeeeee....eeeeeeeeeeee......eeeee..hhhhhhh..eeeeeeeeee.....eeeeeee......---------hhhhheeeeeeeeeehhhhhhh..eeeeeee....eeeeeeee..... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeee----------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cgr L   1 ELVMTQSPLSLPVSLGDQASISCRPSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTAFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    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
(-)
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 2CGR)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2CGR)

 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
    GAS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    LHS  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe H:149 - Pro H:150   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:191 - Pro H:192   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
    Val L:99 - Pro L:100   [ 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
  2cgr
    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
  A2P1G9_MOUSE | A2P1G9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  A2P1G9_MOUSE | A2P1G9
    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
        A2P1G9_MOUSE | A2P1G9: 4zxb
UniProtKB/TrEMBL
        A2P1G9_MOUSE | A2P1G9: 1cgs 1ynk 1ynl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CGR)