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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN
 
Authors :  L. M. Wright, C. D. Reynolds, P. J. Rizkallah, A. K. Allen, E. J. M. Vandamme, M. J. Donovan, W. J. Peumans
Date :  11 Dec 99  (Deposition) - 10 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Two-Domain Lectin, Beta Prism Ii Fold, Native, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Wright, C. D. Reynolds, P. J. Rizkallah, A. K. Allen, E. J. Van Damme, M. J. Donovan, W. J. Peumans
Structural Characterisation Of The Native Fetuin-Binding Protein Scilla Campanulata Agglutinin: A Novel Two-Domain Lectin.
Febs Lett. V. 468 19 2000
PubMed-ID: 10683433  |  Reference-DOI: 10.1016/S0014-5793(00)01109-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN SCAFET PRECURSOR
    Chains: A, B, C, D, E, F
    Organism Scientific: HYACINTHOIDES HISPANICA
    Organism Taxid: 81759
    Other Details: PROTEIN WAS EXTRACTED FROM THE BULBS OF THIS PLANT

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1DLP)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:58
2A:160 -A:183
3B:36 -B:58
4B:160 -B:183
5C:36 -C:58
6C:160 -C:183
7D:36 -D:58
8D:160 -D:183
9E:36 -E:58
10E:160 -E:183
11F:36 -F:58
12F:160 -F:183

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:13 -Pro A:14
2Gly F:104 -Pro F:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DLP)

(-) 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:233
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 256
               SCOP domains d1dlpa1 A:1-115 Fetuin-binding protein Scafet precursor                                                            d1dlpa2 A:116-23  5 Fetuin-binding protein Scafet precursor                                                              SCOP domains
               CATH domains 1dlpA01 A:1-104,A:230-235 Agglutinin, subunit A                                                         1dlpA02 A:105-229 Agglutini  n, subunit A                                                                                    1dlpA0 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee....eeeee.....eeeee...eee.........ee...........ee..................eeee.....eeee..eeee................ee....--......ee...........eeeee...eeeee..................eeeee...eeeeee...eeeee..........eeee.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp A   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYST--NDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|  |   140       150       160       170       180       190       200       210       220       230     
                                                                                                                                                            131  |                                                                                                     
                                                                                                                                                               134                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 256
               SCOP domains d1dlpb1 B:1-113 Fetuin-binding protein Scafet precursor                                                                   d1dlpb2 B:   123-235 Fetuin-binding protein Scafet prec  ursor                                                    SCOP domains
               CATH domains 1dlpB01 B:1-104,B:230-235 Agglutinin, subunit A                                                         1dlpB02 B         :105-229 A   gglutinin, subunit A                                                                          1dlpB0 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee................ee....eeeee.....eeeee...eeee...................eee.....eeee..........eeee.....eeee..........---------..........---................ee..........eee...eee.....--........................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp B   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTS---------NGNSILYSTQ---NHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTA--GTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 235
                                    10        20        30        40        50        60        70        80        90       100       110  |      -  |    130 |   | 140       150       160       170      |180       190       200       210       220       230     
                                                                                                                                          113       123      132 136                                      177  |                                                       
                                                                                                                                                                                                             180                                                       


Chain C from PDB  Type:PROTEIN  Length:234
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:236
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTTG 257
               SCOP domains d1dlpc1 C:1-115 Fetuin-binding protein Scafet precursor                                                            d1dlpc2 C:116-236   Fetuin-binding protein Scafet precursor                                                               SCOP domains
               CATH domains 1dlpC01 C:1-104,C:230-236 Agglutinin, subunit A                                                         1dlpC02 C:105-229 Agglutinin,   subunit A                                                                                    1dlpC01 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................ee..eeeee.....eeee.................................................eeeee...eeeee..eeee................eee.....--.................eeee.....eeee....eeee..........eeeee...eeeee.......ee..........eeeee...eeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp C   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQG--NHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTTG 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  |  | 140       150       160       170       180       190       200       210       220       230      
                                                                                                                                                              133  |                                                                                                    
                                                                                                                                                                 136                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:223
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 256
               SCOP domains d1dlpd1 D:1-114 Fetuin-binding protein Scafet precursor                                                                   d1dlpd2 D    :123-235 Fetuin-binding protein Scafet precursor                                                     SCOP domains
               CATH domains 1dlpD01 D:1-104,D:230-235 Agglutinin, subunit A                                                         1dlpD02 D:        105-229 A    gglutinin, subunit A                                                                          1dlpD0 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...............eeee..eeeee.....eeee....eeee...................eee.....eeee.........eeeee.....eee....eee.....--------...ee....----................eeee.......eeee...eeee..........ee........eee.....eeee...........eee.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp D   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSN--------NGNSILYST----NHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 235
                                    10        20        30        40        50        60        70        80        90       100       110   |     -  |    130|    | 140       150       160       170       180       190       200       210       220       230     
                                                                                                                                           114      123     131  136                                                                                                   


Chain E from PDB  Type:PROTEIN  Length:231
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 256
               SCOP domains d1dlpe1 E:1-115 Fetuin-binding protein Scafet precursor                                                            d1dlpe2 E:116-23    5 Fetuin-binding protein Scafet precursor                                                            SCOP domains
               CATH domains 1dlpE01 E:1-104,E:230-235 Agglutinin, subunit A                                                         1dlpE02 E:105-229 Agglutini    n, subunit A                                                                                  1dlpE0 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee................eeee..eeee.......eeee...eeee....................ee.....eee...........eeeee...eeeee..eeee................ee....----..................eee.....eeeee..ee.............eeeee...eeeeee...eeeee...........eee.....eeee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp E   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYST----NHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|    | 140       150       160       170       180       190       200       210       220       230     
                                                                                                                                                            131  136                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:216
 aligned with Q9ZP48_HYAHI | Q9ZP48 from UniProtKB/TrEMBL  Length:265

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9ZP48_HYAHI    22 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSGTSNKGSVVVANNGNSILYSTQGNDNHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNTAGKGTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 256
               SCOP domains d1dlpf1 F:1-111 Fetuin-binding protein Scafet precursor                                                                    d1dlpf2     F:124-235 Fetuin-binding protein Scafet p   recursor                                                 SCOP domains
               CATH domains 1dlpF01 F:1-104,F:230-235 Agglutinin, subunit A                                                         1dlpF02             F:105-2    29 Agglutinin, subunit A                                                                      1dlpF0 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee................ee....eeeee.....eeeee...eeee.........................................eeeee...eeee.....ee..------------........----................ee..........eee..eeee....---......ee.....ee.....................eee.......eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlp F   1 NNILFGLSHEGSHPQTLHAAQSLELSSFRFTMQSDCNLVLFDSDVRVWASNTAGATGCRAVLQSDGLLVILTAQNTIRWSSGTKGSIGNYVLVLQPDRTVTIYGPGLWDSG------------GNSILYST----NHPQTLHATQSLQLSPYRLSMETDCNLVLFDRDDRVWSTNT---GTGCRAVLQPNGRMDVLTNQNIAVWTSGNSRSAGRYVFVLQPDRNLAIYGGALWTT 235
                                    10        20        30        40        50        60        70        80        90       100       110|        -   |   130|    | 140       150       160       170     | 180       190       200       210       220       230     
                                                                                                                                        111          124    131  136                                     176 180
   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, 12)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 12)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Orthogonal Prism (16)
(-)
Topology: Agglutinin, subunit A (16)
(-)
Homologous Superfamily: Agglutinin, subunit A (16)
(-)
Hyacinthoides hispanica. Organism_taxid: 81759. (2)
1a1dlpB02B:105-229
1b1dlpB01B:1-104,B:230-235
1c1dlpD01D:1-104,D:230-235
1d1dlpE01E:1-104,E:230-235
1e1dlpF01F:1-104,F:230-235
1f1dlpD02D:105-229
1g1dlpF02F:105-229
1h1dlpE02E:105-229
1i1dlpA02A:105-229
1j1dlpC02C:105-229
1k1dlpC01C:1-104,C:230-236
1l1dlpA01A:1-104,A:230-235

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DLP)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1DLP)

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  Cis Peptide Bonds
    Gly F:104 - Pro F:105   [ RasMol ]  
    His A:13 - Pro A:14   [ RasMol ]  
 

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  1dlp
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1b2p STRUCTURE OF THE NATIVE (UNLIGATED) MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7A RESOLUTION. ACTA CRYSTALLOGR., SECT.D D55 PP. 1264 (1999)