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(-) Description

Title :  CRYSTAL STRUCTURE OF SOYBEAN BETA-CONGLYCININ ALPHA PRIME HOMOTRIMER
 
Authors :  Y. Maruyama, N. Maruyama, B. Mikami, S. Utsumi
Date :  16 Jul 03  (Deposition) - 16 Jul 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Double-Stranded Beta-Helix, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Maruyama, N. Maruyama, B. Mikami, S. Utsumi
Structure Of The Core Region Of The Soybean Beta-Conglycini Alpha' Subunit.
Acta Crystallogr. , Sect. D V. 60 289 2004
PubMed-ID: 14747705  |  Reference-DOI: 10.1107/S0907444903027367

(-) Compounds

Molecule 1 - ALPHA PRIME SUBUNIT OF BETA-CONGLYCININ
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 142-559
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: SEED STORAGE PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1026 , HOH A:1082 , HOH A:1116 , HOH A:1171 , HOH B:1011 , HOH B:1143BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREHOH A:1026 , HOH A:1082 , HOH A:1116 , HOH A:1171 , HOH B:1011 , HOH B:1143BINDING SITE FOR RESIDUE MG B 1002
3AC3SOFTWAREHOH C:1020 , HOH C:1156 , HOH C:1157BINDING SITE FOR RESIDUE MG C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UIK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UIK)

(-) 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:364
 aligned with Q7XXT2_SOYBN | Q7XXT2 from UniProtKB/TrEMBL  Length:621

    Alignment length:388
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589        
         Q7XXT2_SOYBN   210 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFGREEGQQQGEERLQESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGIKEQQQRQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 597
               SCOP domains d1uika1 A:148-350 Seed storage 7S protein                                                                                                                                                                  d1uika2 A:351-535 Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1uikA01 A:148-348 Jelly Rolls                                                                                                                                                                            1uikA02 A:349-535 Jelly Rolls                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhh.eeeeee...eeeeee......hhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee.eeeeeee....eeeeeee..eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh..------------....eee.hhhhhhhhh......hhhhhhh....ee.......ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeee.------------....eeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uik A 148 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFG------------QESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGI------------PLEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 535
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     |   -       327       337       347       357       367       377       387       397       407       417       427   |     -      |447       457       467       477       487       497       507       517       527        
                                                                                                                                                                                               313          326                                                                                                      431          444                                                                                           


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with Q7XXT2_SOYBN | Q7XXT2 from UniProtKB/TrEMBL  Length:621

    Alignment length:388
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589        
         Q7XXT2_SOYBN   210 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFGREEGQQQGEERLQESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGIKEQQQRQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 597
               SCOP domains d1uikb1 B:148-350 Seed storage 7S protein                                                                                                                                                                  d1uikb2 B:351-535 Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1uikB01 B:148-348 Jelly Rolls                                                                                                                                                                            1uikB02 B:349-535 Jelly Rolls                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhh.eeeeee...eeeeee.........hhhhh..eeeeeee...eeeeeeee.eeeeeeeee.eeeeeee....eeeeeee..eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh..------------....eee.hhhhhhhh.......hhhhh......ee.......ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeee.-------------...eeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uik B 148 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFG------------QESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGI-------------LEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 535
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     |   -       327       337       347       357       367       377       387       397       407       417       427   |     -       447       457       467       477       487       497       507       517       527        
                                                                                                                                                                                               313          326                                                                                                      431           445                                                                                          


Chain C from PDB  Type:PROTEIN  Length:364
 aligned with Q7XXT2_SOYBN | Q7XXT2 from UniProtKB/TrEMBL  Length:621

    Alignment length:388
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589        
         Q7XXT2_SOYBN   210 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFGREEGQQQGEERLQESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGIKEQQQRQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 597
               SCOP domains d1uikc1 C:148-350 Seed storage 7S protein                                                                                                                                                                  d1uikc2 C:351-535 Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1uikC01 C:148-348 Jelly Rolls                                                                                                                                                                            1uikC02 C:349-535 Jelly Rolls                                                                                                                                                               CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC01 C:360-535                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC02 C:360-535                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC03 C:360-535                                                                                                                                                        Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC04 C:360-535                                                                                                                                                        Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC05 C:360-535                                                                                                                                                        Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------            ----------------------------------Cupin_1-1uikC06 C:360-535                                                                                                                                                        Pfam domains (6)
         Sec.struct. author ...eehhh.eeeeee...eeeeee......hhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee.eeeeeee....eeeeeee..eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh..------------....eee.hhhhhhhhh......hhhhhhh....ee.......eee..eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeee.------------....eeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uik C 148 NPFHFNSKRFQTLFKNQYGHVRVLQRFNKRSQQLQNLRDYRILEFNSKPNTLLLPHHADADYLIVILNGTAILTLVNNDDRDSYNLQSGDALRVPAGTTYYVVNPDNDENLRMITLAIPVNKPGRFESFFLSSTQAQQSYLQGFSKNILEASYDTKFEEINKVLFG------------QESVIVEISKKQIRELSKHAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKLFEITPEKNPQLRDLDVFLSVVDMNEGALFLPHFNSKAIVVLVINEGEANIELVGI------------PLEVRKYRAELSEQDIFVIPAGYPVVVNATSDLNFFAFGINAENNQRNFLAGSKDNVISQIPSQVQELAFPGSAKDIENLIKSQSESYFVDA 535
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     |   -       327       337       347       357       367       377       387       397       407       417       427   |     -      |447       457       467       477       487       497       507       517       527        
                                                                                                                                                                                               313          326                                                                                                      431          444
   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)
1a1uikB02B:349-535
1b1uikA02A:349-535
1c1uikC02C:349-535
1d1uikA01A:148-348
1e1uikB01B:148-348
1f1uikC01C:148-348

(-) 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   (Q7XXT2_SOYBN | Q7XXT2)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

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(-) Related Entries Specified in the PDB File

1uij 1UIJ CONTAINS BETA SUBUNIT OF BETA-CONGLYCININ(I122M/K124W)