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

(-) Description

Title :  CRYSTAL STRUCTURE OF PROGLYCININ MUTANT C88S
 
Authors :  S. Utsumi, M. Adachi
Date :  24 Apr 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Glycinin, Soybean, Trimer, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Adachi, E. Okuda, Y. Kaneda, A. Hashimoto, A. D. Shutov, C. Becker, S. Utsumi
Crystal Structures And Structural Stabilities Of The Disulfide Bond-Deficient Soybean Proglycinin Mutants C12G And C88S.
J. Agric. Food Chem. V. 51 4633 2003
PubMed-ID: 14705889  |  Reference-DOI: 10.1021/JF026065Y
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCININ G1
    ChainsA, B, C
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    MutationYES
    Organism CommonSOYBEAN
    Organism ScientificGLYCINE MAX
    Organism Taxid3847
    SynonymPROGLYCININ

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UD1)

(-) Sites  (0, 0)

(no "Site" information available for 1UD1)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:45
2B:12 -B:45
3C:12 -C:45

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:408 -Asn A:409
2Asp B:408 -Asn B:409
3Asp C:408 -Asn C:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UD1)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
111S_SEED_STORAGEPS00305 11-S plant seed storage proteins signature.GLYG1_SOYBN310-332
 
 
  3A:297-313
B:297-313
C:297-313

(-) Exons   (0, 0)

(no "Exon" information available for 1UD1)

(-) 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 A from PDB  Type:PROTEIN  Length:366
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:461
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
          GLYG1_SOYBN    29 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ud1a1 A:10-248 Seed storage 7S protein                                                                                                                                                                                                                                                       d1ud1a2 A:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains ------------1ud1A01 A:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ud1A02 A:307-470 Jelly Rolls                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...eeeee....hhhhhhhh.eeeeeee...eeeeeeee...eeeeeee..eeeeee..-----------------------....eeee...eeeee....eeeeee.....eeeeeee..............eee........hhhhhh-------------------...hhhhhhhhhhhhhhh.hhhhhhh....-----...eee..........------------------------------------------------......eee........eee...eeeeee......hhhhhh..eeeeee....eeeeeee....eeeeeee.eeeeeee.......eeeeee...eeee....eeeeee....eeeeeee......eee......hhhhhhhhhhhhhhh.hhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ud1 A  10 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYP-----------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    19        29        39        49        59        69        79      |  -         -         -|      119       129       139       149       159       169        |-         -       199       209       219       | -   |   239        |-         -         -         -         -       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469 
                                                                                                       86                     110                                                                 178                 198                          227   233            248                                              297                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:366
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:461
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
          GLYG1_SOYBN    29 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ud1b1 B:10-248 Seed storage 7S protein                                                                                                                                                                                                                                                       d1ud1b2 B:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains ------------1ud1B01 B:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ud1B02 B:307-470 Jelly Rolls                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..eeeee....hhhhhhhh.eeeeeee...eeeeeee....eeeeeee.eeeeeee..-----------------------....eeeee..eeeee....eeeee......eeeeeee...............ee........hhhhhh-------------------...hhhhhhhhhhhhhhh.hhhhhhhhh..-----...eee..........------------------------------------------------......eee........eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeee..eeeeee.....eeeee......eeee....eeeeee....eeeeeee......eee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ud1 B  10 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYP-----------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    19        29        39        49        59        69        79      |  -         -         -|      119       129       139       149       159       169        |-         -       199       209       219       | -   |   239        |-         -         -         -         -       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469 
                                                                                                       86                     110                                                                 178                 198                          227   233            248                                              297                                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:366
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:461
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
          GLYG1_SOYBN    29 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ud1c1 C:10-248 Seed storage 7S protein                                                                                                                                                                                                                                                       d1ud1c2 C:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains ------------1ud1C01 C:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ud1C02 C:307-470 Jelly Rolls                                                                                                                                        CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C01 C:304-453                                                                                                                             ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C02 C:304-453                                                                                                                             ----------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C03 C:304-453                                                                                                                             ----------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C04 C:304-453                                                                                                                             ----------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C05 C:304-453                                                                                                                             ----------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ud1C06 C:304-453                                                                                                                             ----------------- Pfam domains (6)
         Sec.struct. author ..............eeeee..eeeee....hhhhhhhh.eeeeeee...eeeeeee....eeeeeee..eeeeee..-----------------------....eeee...eeeee....eeeeee.....eeeeeee...............ee........hhhhhh-------------------........hhhhhhhhhh.hhhhhhhhh..-----...eee..........------------------------------------------------......eee........eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeee..eeeeee.....eeeeeee....eeee....eeeeee....eeeeeee......eee...........hhhhhhhhhh...hhhhhhh.......ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ud1 C  10 NECQIQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYP-----------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    19        29        39        49        59        69        79      |  -         -         -|      119       129       139       149       159       169        |-         -       199       209       219       | -   |   239        |-         -         -         -         -       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469 
                                                                                                       86                     110                                                                 178                 198                          227   233            248                                              297                                                                                                                                                                             

   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  (1, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a1ud1A02A:307-470
1b1ud1B02B:307-470
1c1ud1C02C:307-470
1d1ud1A01A:22-306
1e1ud1B01B:22-306
1f1ud1C01C:22-306

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (GLYG1_SOYBN | P04776)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

 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
(no "Ligands, Modified Residues, Ions" information available for 1ud1)
 
  Sites
(no "Sites" information available for 1ud1)
 
  Cis Peptide Bonds
    Asp A:408 - Asn A:409   [ RasMol ]  
    Asp B:408 - Asn B:409   [ RasMol ]  
    Asp C:408 - Asn C:409   [ 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
  1ud1
    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
  GLYG1_SOYBN | P04776
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  GLYG1_SOYBN | P04776
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GLYG1_SOYBN | P047761fxz 1ucx

(-) Related Entries Specified in the PDB File

1fxz WILD-TYPE PROGLYCININ
1ucx C12G MUTANT PROGLYCININ