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(-) Description

Title :  CRYSTAL STRUCTURE OF ADZUKI BEAN 7S GLOBULIN-3
 
Authors :  T. Fukuda, B. Mikami, S. Utsumi
Date :  31 Jan 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
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-3
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEADZUKI7S3
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET-21D
    Gene: 7S-3
    Organism Common: ADZUKI BEAN
    Organism Scientific: VIGNA ANGULARIS
    Organism Taxid: 3914

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CA3Ligand/IonCALCIUM ION
3CIT3Ligand/IonCITRIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:382 , PHE A:385 , PRO A:386 , ALA A:387 , HOH A:1375 , HOH C:1354BINDING SITE FOR RESIDUE CA A 906
2AC2SOFTWAREHOH A:1400 , GLU B:382 , PHE B:385 , PRO B:386 , ALA B:387BINDING SITE FOR RESIDUE CA B 905
3AC3SOFTWAREGLU C:382 , PHE C:385 , PRO C:386 , ALA C:387BINDING SITE FOR RESIDUE CA C 904
4AC4SOFTWAREARG A:46 , ASN A:142 , HIS A:144 , ARG A:145BINDING SITE FOR RESIDUE CIT A 1285
5AC5SOFTWAREARG B:46 , GLN B:49 , ASN B:142 , HIS B:144 , ARG B:145BINDING SITE FOR RESIDUE CIT B 1284
6AC6SOFTWARELYS A:52 , GLN A:55 , ARG C:46 , ASN C:142 , HIS C:144 , ARG C:145BINDING SITE FOR RESIDUE CIT C 1283
7AC7SOFTWARETRP A:249 , HIS A:281 , ASN A:283 , ILE A:334 , ARG A:362BINDING SITE FOR RESIDUE ACY A 460
8AC8SOFTWARETRP B:249 , HIS B:281 , ASN B:283 , VAL B:288 , ILE B:334BINDING SITE FOR RESIDUE ACY B 461
9AC9SOFTWARETRP C:249 , HIS C:281 , ASN C:283 , ARG C:362BINDING SITE FOR RESIDUE ACY C 462

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln C:408 -Pro C:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EAA)

(-) 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:375
 aligned with A4PIA0_PHAAN | A4PIA0 from UniProtKB/TrEMBL  Length:433

    Alignment length:396
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403      
         A4PIA0_PHAAN    14 DSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2eaaA01 A:14-209 Jelly Rolls                                                                                                                                                                        ------------     ----2eaaA02 A:231-404 Jelly Rolls                                                                                                                                                 ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.hhh..ee.....eeeeeee..eeeeee.hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee.eeeeeeee..eeeeeeee..eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh...--------.......eee.hhhhhhhhhhhh...-----......ee.hhh...eee..eeeeeehhhhhhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeee..--------....eeeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eaa A  14 DSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGE--------ESREEGVIVELKREQIQELMKHAKSS-----SSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSD--------ESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   |     -  |    203       213       | -   |   233       243       253       263       273       283       293       303  |      - |     323       333       343       353       363       373       383       393       403      
                                                                                                                                                                                                       187      196                      221   227                                                                            306      315                                                                                              


Chain B from PDB  Type:PROTEIN  Length:380
 aligned with A4PIA0_PHAAN | A4PIA0 from UniProtKB/TrEMBL  Length:433

    Alignment length:397
                                    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       
         A4PIA0_PHAAN    13 SDSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2eaaB01 B:13-209 Jelly Rolls                                                                                                                                                                         ---------------------2eaaB02 B:231-404 Jelly Rolls                                                                                                                                                 ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh..ee.....eeeeeee..eeeeee.hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh..-------........eee.hhhhhhhh..................ee.hhh...ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeee..----------..eeeeeeee....eeee.....eeeee...eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eaa B  13 SDSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGE-------EESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSD----------LEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
                                    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     195                                                                                                            306        317                                                                                            


Chain C from PDB  Type:PROTEIN  Length:377
 aligned with A4PIA0_PHAAN | A4PIA0 from UniProtKB/TrEMBL  Length:433

    Alignment length:397
                                    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       
         A4PIA0_PHAAN    13 SDSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEERQQQQGEESREEGVIVELKREQIQELMKHAKSSSRKELSSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSDQQQQKQQEESLEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2eaaC01 C:13-209 Jelly Rolls                                                                                                                                                                         -------------    ----2eaaC02 C:231-404 Jelly Rolls                                                                                                                                                 ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhh..ee.....eeeeeee..eeeeee.hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeeee..eeeeeee...eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh...-------.......eee.hhhhhhhhhhhhee..----......ee.hhh...ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeee..-------.--..eeeeeeee....eeee.....eeeee...eeeeeeee......eee......hhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eaa C  13 SDSRGENNPFYFSSDRRFHTLFTNQYGHLRILHRFDQRSKQIQNLENYRVVEFKSKPNTLLLPHHADADFLLVVLNGRAILTLVNPDSRDSYILEQGHAQKIPAGTTFFLVNPDDNENLRIIKLAIPVNNPHRFQDFFLSSTEAQQSYLRGFSKNILEASFDSDFKEINRVLFGEE-------ESREEGVIVELKREQIQELMKHAKSSS----SSQDEPFNLRNSKPIYSNKFGRWYEMTPEKNPQLKDLDVFISSVDMKEGALLLPHYNSKAIVIMVINEGEAKIELVGLSD-------E--LEVQRYRAELSEDDVFVIPAAYPVAINATSNLNFFAFGINAENNQRNFLAGGKDNVMSEIPTEVLEVSFPASGKKVEKLIKKQSESHFVDAQP 409
                                    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       
                                                                                                                                                                                                         188     196                       222  227                                                                            306     314  |                                                                                            
                                                                                                                                                                                                                                                                                                                                          317
   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 2EAA)

(-) 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)
1a2eaaB02B:231-404
1b2eaaB01B:13-209
1c2eaaC01C:13-209
1d2eaaC02C:231-404
1e2eaaA02A:231-404
1f2eaaA01A:14-209

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (A4PIA0_PHAAN | A4PIA0)
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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 Related Entries

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(-) Related Entries Specified in the PDB File

2ea7 THE ISOTYPE OF ADZUKI BEAN 7S GLOBULIN-1.