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 C12G MUTANT
 
Authors :  S. Utsumi, M. Adachi
Date :  24 Apr 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Proglycinin, Soybean, Trimer, Mutant, 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
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: PROGLYCININ

 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 1UCX)

(-) Sites  (0, 0)

(no "Site" information available for 1UCX)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:88 -A:298
2B:88 -B:298
3C:88 -C:298

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UCX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1UCX)

(-) 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:367
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:457
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
          GLYG1_SOYBN    33 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ucxa1 A:14-248 Seed storage 7S protein                                                                                                                                                                                                                                                   d1ucxa2 A:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains --------1ucxA01 A:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ucxA02 A:307-470 Jelly Rolls                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..eeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeee..eeeee........------------------....eeee...eeeee.....eeeee.....eeeeeeee.............eee..............-------------------...hhhhhhhhhhhhhhh.hhhhhhhhh..-----...eee..........------------------------------------------------.......ee........eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeee.eeeeeee.....eeeeeeee...eeee....eeeeee....eeeeeee......eee......hhhhhhhhhhhhhhh...hhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucx A  14 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPST------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    23        33        43        53        63        73        83       | -         -      |113       123       133       143       153       163       173    |    -         -    |  203       213       223   |   233       243    |    -         -         -         -         -   |   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       
                                                                                                        91                110                                                                 178                 198                          227   233            248                                              297                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:367
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:457
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
          GLYG1_SOYBN    33 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ucxb1 B:14-248 Seed storage 7S protein                                                                                                                                                                                                                                                   d1ucxb2 B:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains --------1ucxB01 B:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ucxB02 B:307-470 Jelly Rolls                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeee....hhhhhhhh.eeeeeee...eeeeeeee...eeeeeee.eeeeeee.......------------------....eeeee..eeeee....eeeee......eeeeeee..............eee........hhhhhh-------------------........hhhhhhhhhh.hhhhhhhhh..-----...eee..........------------------------------------------------......eee........eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeee..eeeeee.......eee......eeee....eeeeee....eeeeeee......eee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucx B  14 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPST------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    23        33        43        53        63        73        83       | -         -      |113       123       133       143       153       163       173    |    -         -    |  203       213       223   |   233       243    |    -         -         -         -         -   |   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       
                                                                                                        91                110                                                                 178                 198                          227   233            248                                              297                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:367
 aligned with GLYG1_SOYBN | P04776 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:457
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
          GLYG1_SOYBN    33 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPSTFEEPQQPQQRGQSSRPQDRHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQEQGGHQSQKGKHQQEEENEGGSILSGFTLEFLEHAFSVDKQIAKNLQGENEGEDKGAIVTVKGGLSVIKPPTDEQQQRPQEEEEEEEDEKPQCKGKDKHCQRPRGSQSKSRRNGIDETICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 489
               SCOP domains d1ucxc1 C:14-248 Seed storage 7S protein                                                                                                                                                                                                                                                   d1ucxc2 C:297-470 Seed storage 7S protein                                                                                                                                      SCOP domains
               CATH domains --------1ucxC01 C:22-306 Jelly Rolls                                                                                                                                                                                                                                                                 1ucxC02 C:307-470 Jelly Rolls                                                                                                                                        CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC01 C:304-453                                                                                                                             ----------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC02 C:304-453                                                                                                                             ----------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC03 C:304-453                                                                                                                             ----------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC04 C:304-453                                                                                                                             ----------------- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC05 C:304-453                                                                                                                             ----------------- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cupin_1-1ucxC06 C:304-453                                                                                                                             ----------------- Pfam domains (6)
         Sec.struct. author ..........eeeee..eeeee....hhhhhhhh.eeeeeee...eeeeeeee...eeeeeee.eeeeeee.......------------------....eeeee..eeeee....eeeeee.....eeeeeee..............eee........hhhhhh-------------------........hhhhhhhhhh.hhhhhhhhh..-----...eee..........------------------------------------------------......eee........eee...eeeeee......hhhhhh..eeeeee....eeeeeee....eeeeeee.eeeeeee.......eeeeee..eeeee....eeeeee....eeeeeee......eee.............hhhhhhhh.hhhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------11S_SEED_STORAGE       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucx C  14 IQKLNALKPDNRIESEGGLIETWNPNNKPFQCAGVALSRCTLNRNALRRPSYTNGPQEIYIQQGKGIFGMIYPGCPST------------------RHQKIYNFREGDLIAVPTGVAWWMYNNEDTPVVAVSIIDTNSLENQLDQMPRRFYLAGNQEQEFLKYQQ-------------------GGSILSGFTLEFLEHAFSVDKQIAKNLQGE-----KGAIVTVKGGLSVIKP------------------------------------------------ICTMRLRHNIGQTSSPDIYNPQAGSVTTATSLDFPALSWLRLSAEFGSLRKNAMFVPHYNLNANSIIYALNGRALIQVVNCNGERVFDGELQEGRVLIVPQNFVVAARSQSDNFEYVSFKTNDTPMIGTLAGANSLLNALPEEVIQHTFNLKSQQARQIKNNNPFKFLVPPQES 470
                                    23        33        43        53        63        73        83       | -         -      |113       123       133       143       153       163       173    |    -         -    |  203       213       223   |   233       243    |    -         -         -         -         -   |   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       
                                                                                                        91                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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: Jelly Rolls (177)
(-)
Soybean (Glycine max) (10)
1a1ucxA02A:307-470
1b1ucxA01A:22-306
1c1ucxB01B:22-306
1d1ucxC01C:22-306
1e1ucxB02B:307-470
1f1ucxC02C:307-470

(-) 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 1ucx)
 
  Sites
(no "Sites" information available for 1ucx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ucx)
 

(-) 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 ](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
  1ucx
    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
  GLYG1_SOYBN | P04776
    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
  GLYG1_SOYBN | P04776
    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
        GLYG1_SOYBN | P04776: 1fxz 1ud1

(-) Related Entries Specified in the PDB File

1fxz WILD-TYPE PROGLYCININ
1ud1 C88S MUTANT PROGLYCININ