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(-) Description

Title :  STRUCTURE ANALYSIS OF A WOUND-INDUCIBLE LECTIN IPOMOELIN FROM SWEET POTATO
 
Authors :  K. L. Liu, W. C. Chang, S. T. Jeng, Y. S. Cheng
Date :  18 Mar 11  (Deposition) - 28 Mar 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E  (4x)
Keywords :  Beta Prism, Carbohydrate/Sugar Binding, Carbohydrate-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Chang, K. L. Liu, F. C. Hsu, S. T. Jeng, Y. S. Cheng
Ipomoelin, A Jacalin-Related Lectin With A Compact Tetrameric Association And Versatile Carbohydrate Binding Properties Regulated By Its N Terminus.
Plos One V. 7 40618 2012
PubMed-ID: 22808208  |  Reference-DOI: 10.1371/JOURNAL.PONE.0040618

(-) Compounds

Molecule 1 - IPOMOELIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTZ18UH-IPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IPOMOELIN
    Organism Common: BATATE
    Organism Scientific: IPOMOEA BATATAS
    Organism Taxid: 4120

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCD 
Biological Unit 2 (4x):     E

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3R50)

(-) Sites  (0, 0)

(no "Site" information available for 3R50)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R50)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Gly A:14 -Pro A:15
2Asn A:57 -Pro A:58
3Gly A:113 -Pro A:114
4Gly B:14 -Pro B:15
5Asn B:57 -Pro B:58
6Gly B:113 -Pro B:114
7Gly C:14 -Pro C:15
8Asn C:57 -Pro C:58
9Gly C:113 -Pro C:114
10Gly D:14 -Pro D:15
11Gly D:113 -Pro D:114
12Gly E:14 -Pro E:15
13Asn E:57 -Pro E:58
14Gly E:113 -Pro E:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R50)

(-) Exons   (0, 0)

(no "Exon" information available for 3R50)

(-) Sequences/Alignments

Asymmetric 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:153
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
         P93193_IPOBA     2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r50a_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeeee...eeeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee..eeeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r50 A   2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
         P93193_IPOBA     1 MALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r50b_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee.eeeeeee....eeeeee......eeeeeee.......eeeeeeeee...eeeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r50 B   1 MALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
         P93193_IPOBA     2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r50c_ C: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeeee...eeeeee........eeeeee......eeeeeeeee..eeeeeeeeee....eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r50 C   2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


Chain D from PDB  Type:PROTEIN  Length:153
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
         P93193_IPOBA     2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r50d_ D: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee.eeeeeee....eeeeee......eeeeeeeee...eeeeeeeeeeee..eeeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r50 D   2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   


Chain E from PDB  Type:PROTEIN  Length:151
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 
         P93193_IPOBA     4 QLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r50e_ E: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....eeeee.......eeeeeeee.....eeeeeeeeee...eeeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r50 E   4 QLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
   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, 5)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R50)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3R50)

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  Cis Peptide Bonds
    Asn A:57 - Pro A:58   [ RasMol ]  
    Asn B:57 - Pro B:58   [ RasMol ]  
    Asn C:57 - Pro C:58   [ RasMol ]  
    Asn E:57 - Pro E:58   [ RasMol ]  
    Gly A:113 - Pro A:114   [ RasMol ]  
    Gly A:14 - Pro A:15   [ RasMol ]  
    Gly B:113 - Pro B:114   [ RasMol ]  
    Gly B:14 - Pro B:15   [ RasMol ]  
    Gly C:113 - Pro C:114   [ RasMol ]  
    Gly C:14 - Pro C:15   [ RasMol ]  
    Gly D:113 - Pro D:114   [ RasMol ]  
    Gly D:14 - Pro D:15   [ RasMol ]  
    Gly E:113 - Pro E:114   [ RasMol ]  
    Gly E:14 - Pro E:15   [ RasMol ]  
 
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  3r50
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 Related Entries

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

UniProtKB/TrEMBL
        P93193_IPOBA | P93193: 3r51 3r52 4ddn

(-) Related Entries Specified in the PDB File

3r51 IPO-MMP COMPLEX
3r52 IPO-MGP COMPLEX
3r53 IPO-SIA COMPLEX