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(-) Description

Title :  STRUCTURE ANALYSIS OF A WOUND-INDUCIBLE LECTIN IPOMOELIN FROM SWEET POTATO
 
Authors :  W. C. Chang, K. L. Liu, S. T. Jeng, F. C. Hsu, Y. S. Cheng
Date :  19 Jan 12  (Deposition) - 01 Aug 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Prism, Carbohydrate Binding Protein, Carbohydrate/Sugar Binding, Sugar 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
    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
    Organism Common: BATATE
    Organism Scientific: IPOMOEA BATATAS
    Organism Taxid: 4120

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1AMG4Ligand/IonALPHA-METHYL-D-GALACTOSIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , GLY A:21 , TYR A:97 , GLY A:141 , TRP A:142 , TYR A:143 , ASP A:145 , ASP C:129BINDING SITE FOR RESIDUE AMG A 200
2AC2SOFTWAREGLY B:20 , GLY B:21 , TYR B:97 , GLY B:141 , TRP B:142 , TYR B:143 , ASP B:145BINDING SITE FOR RESIDUE AMG B 200
3AC3SOFTWAREGLY C:20 , GLY C:21 , TYR C:97 , GLY C:141 , TRP C:142 , TYR C:143 , ASP C:145 , HOH C:332BINDING SITE FOR RESIDUE AMG C 200
4AC4SOFTWAREGLY D:20 , GLY D:21 , TYR D:97 , GLY D:141 , TRP D:142 , TYR D:143 , ASP D:145 , HOH D:352BINDING SITE FOR RESIDUE AMG D 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DDN)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological 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
11Asn D:57 -Pro D:58
12Gly D:113 -Pro D:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DDN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DDN)

(-) Exons   (0, 0)

(no "Exon" information available for 4DDN)

(-) 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: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 d4ddna_ 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...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddn A   1 MALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    


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 d4ddnb_ B: 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...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddn 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: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 d4ddnc_ C: 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...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddn C   1 MALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    


Chain D 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 d4ddnd_ D: 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...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddn D   1 MALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DDN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DDN)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DDN)

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 Related Entries

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

UniProtKB/TrEMBL
        P93193_IPOBA | P93193: 3r50 3r51 3r52

(-) Related Entries Specified in the PDB File

3r50 APO FORM OF IPO
3r51 IPO-MEMAN COMPLEX
3r52 IPO-MEGLC COMPLEX