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(-) Description

Title :  CRYSTAL STRUCTURE OF ADZUKI BEAN 7S GLOBULIN-1
 
Authors :  T. Fukuda, B. Mikami, S. Utsumi
Date :  30 Jan 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Beta Barrel, Cupin Superfamily, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fukuda, N. Maruyama, M. R. Salleh, B. Mikami, S. Utsumi
Characterization And Crystallography Of Recombinant 7S Globulins Of Adzuki Bean And Structure-Function Relationships With 7S Globulins Of Various Crops.
J. Agric. Food Chem. V. 56 4145 2008
PubMed-ID: 18461964  |  Reference-DOI: 10.1021/JF072667B

(-) Compounds

Molecule 1 - 7S GLOBULIN-1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21D, PEADZUKI7S1
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 7S-1
    Organism Common: ADZUKI BEAN
    Organism Scientific: VIGNA ANGULARIS
    Organism Taxid: 3914
    Strain: CULTIVAR, DAINAGON

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CA4Ligand/IonCALCIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:383 , PHE A:386 , PRO A:387 , ALA A:388 , HOH A:674 , HOH C:613BINDING SITE FOR RESIDUE CA A 450
2AC2SOFTWAREHOH A:624 , GLU B:383 , PHE B:386 , PRO B:387 , ALA B:388BINDING SITE FOR RESIDUE CA B 452
3AC3SOFTWAREASN B:71 , PRO B:126 , ASP B:128BINDING SITE FOR RESIDUE CA B 453
4AC4SOFTWAREGLU C:383 , PHE C:386 , PRO C:387 , ALA C:388 , HOH C:592 , HOH C:646BINDING SITE FOR RESIDUE CA C 451
5AC5SOFTWARELEU A:279 , HIS A:282 , ILE A:335 , PHE A:351 , HOH A:485BINDING SITE FOR RESIDUE ACY A 460
6AC6SOFTWARETRP B:250 , HIS B:282 , VAL B:289 , ILE B:335 , HOH B:671BINDING SITE FOR RESIDUE ACY B 461
7AC7SOFTWARELEU C:279 , HIS C:282 , ILE C:335 , HOH C:622 , HOH C:623BINDING SITE FOR RESIDUE ACY C 462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EA7)

(-) Exons   (0, 0)

(no "Exon" information available for 2EA7)

(-) 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:390
 aligned with A4PI98_PHAAN | A4PI98 from UniProtKB/TrEMBL  Length:434

    Alignment length:399
                                    22        32        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         
         A4PI98_PHAAN    13 VSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQPE 411
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ea7A01 A:13-210 Jelly Rolls                                                                                                                                                                          ---------------------2ea7A02 A:232-405 Jelly Rolls                                                                                                                                                 ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhh..ee.....eeeeeee..eeeeee......hhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee.eeeeeee....eeeeeee..eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh.---------.......eee.hhhhhhhhhh................ee.......eee..eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeeeee..........eeeeeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhh......eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ea7 A  13 VSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFG---------ESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQPE 411
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    |    -    |  202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402         
                                                                                                                                                                                                        187       197                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:382
 aligned with A4PI98_PHAAN | A4PI98 from UniProtKB/TrEMBL  Length:434

    Alignment length:399
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400         
         A4PI98_PHAAN    11 EEVSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQ 409
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ea7B01 B:11-210 Jelly Rolls                                                                                                                                                                            ---------------  ----2ea7B02 B:232-405 Jelly Rolls                                                                                                                                                 ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhh..ee.....eeeeeee..eeeeee......hhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh..---------......eee.hhhhhhh...........--......ee.......eee..eeeeeehhhhhhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeee..------......eeeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ea7 B  11 EEVSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGE---------SREEGVIVELKREQIQELMKHAKSSSRK--SSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSD------QEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQ 409
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -       200       210       220    |  230       240       250       260       270       280       290       300      |  -   |   320       330       340       350       360       370       380       390       400         
                                                                                                                                                                                                           188       198                        225  |                                                                            307    314                                                                                               
                                                                                                                                                                                                                                                   228                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:379
 aligned with A4PI98_PHAAN | A4PI98 from UniProtKB/TrEMBL  Length:434

    Alignment length:398
                                    22        32        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        
         A4PI98_PHAAN    13 VSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 410
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ea7C01 C:13-210 Jelly Rolls                                                                                                                                                                          ---------------  ----2ea7C02 C:232-405 Jelly Rolls                                                                                                                                                 ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh..ee.....eeeeeee..eeeeee......hhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeeee..eeeeeee...eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh.----------......eee.hhhhhhhhhh........--......ee.......ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee.eeeeeeeeee.-------....eeeeeeeeee...eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ea7 C  13 VSVSSGKNNPFYFNSDRWFRTLYRNEWGHIRVLQRFDQRSKQMQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGTAVLTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFG----------SREEGVIVELKREQIQELMKHAKSSSRK--SSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYSSKAIVIMVINEGEAKIELVGLSD-------EESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNRRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 410
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    |    -     | 202       212       222  |  | 232       242       252       262       272       282       292       302    |    -  |    322       332       342       352       362       372       382       392       402        
                                                                                                                                                                                                        187        198                        225  |                                                                            307     315                                                                                               
                                                                                                                                                                                                                                                 228
   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  (0, 0)

(no "SCOP Domain" information available for 2EA7)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: Jelly Rolls (177)
(-)
Adzuki bean (Vigna angularis) (2)
1a2ea7C02C:232-405
1b2ea7B02B:232-405
1c2ea7A02A:232-405
1d2ea7C01C:13-210
1e2ea7A01A:13-210
1f2ea7B01B:11-210

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EA7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (A4PI98_PHAAN | A4PI98)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

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  2ea7
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 Related Entries

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(-) Related Entries Specified in the PDB File

2eaa