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(-) Description

Title :  THE CRYSTAL STRUCTURES OF TWO FRAGMENTS TRUNCATED FROM 5-BLADED BETA-PROPELLER LECTIN, TACHYLECTIN-2 (LIB1-B7-18 AND LIB2-D2-15)
 
Authors :  O. Dym, D. S. Tawfik, I. Yadid, Israel Structural Proteomics Center
Date :  02 Nov 09  (Deposition) - 28 Apr 10  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J  (1x)
Biol. Unit 2:  A,B,C,D,E  (1x)
Biol. Unit 3:  F,G,H,I,J  (1x)
Keywords :  5-Bladed -Propeller, Structural Genomics, Israel Structural Proteomics Center, Ispc, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Yadid, N. Kirshenbaum, M. Sharon, O. Dym, D. S. Tawfik
Metamorphic Proteins Mediate Evolutionary Transitions Of Structure
Proc. Natl. Acad. Sci. Usa V. 107 7287 2010
PubMed-ID: 20368465  |  Reference-DOI: 10.1073/PNAS.0912616107

(-) Compounds

Molecule 1 - 5-BLADED BETA-PROPELLER LECTIN
    ChainsA, B, C, D, E, F, G, H, I, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 1-106
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SynonymTACHYLECTIN-2

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit ABCDEFGHIJ
Biological Unit 1 (1x)ABCDEFGHIJ
Biological Unit 2 (1x)ABCDE     
Biological Unit 3 (1x)     FGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GDL9Ligand/Ion2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1GDL9Ligand/Ion2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GDL5Ligand/Ion2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1GDL4Ligand/Ion2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:22 , ASN A:23 , GLY A:24 , GLY A:25 , TRP A:26 , ASP A:57 , ASN A:60 , TRP A:61 , ILE A:62BINDING SITE FOR RESIDUE GDL A 110
02AC2SOFTWAREGLY B:22 , ASN B:23 , GLY B:24 , TRP B:26 , ASP B:57 , ASN B:60 , TRP B:61 , ILE B:62 , HOH B:109 , SER I:52BINDING SITE FOR RESIDUE GDL B 110
03AC3SOFTWARESER C:70 , GLY C:71 , GLY C:72 , TRP C:73 , ASN D:13 , TRP D:14BINDING SITE FOR RESIDUE GDL D 241
04AC4SOFTWAREGLY D:22 , ASN D:23 , GLY D:24 , TRP D:26 , ASP D:57 , ASN D:60 , TRP D:61 , ILE D:62BINDING SITE FOR RESIDUE GDL D 238
05AC5SOFTWAREGLY E:22 , ASN E:23 , GLY E:24 , GLY E:25 , TRP E:26 , ASP E:57 , ASN E:60 , TRP E:61 , ILE E:62BINDING SITE FOR RESIDUE GDL E 110
06AC6SOFTWAREARG E:91 , GLY E:92 , GLN E:93 , ARG E:94BINDING SITE FOR RESIDUE SO4 E 107
07AC7SOFTWAREGLY F:22 , ASN F:23 , GLY F:24 , TRP F:26 , PHE F:29 , ASP F:57 , ASN F:60 , TRP F:61 , ILE F:62BINDING SITE FOR RESIDUE GDL F 110
08AC8SOFTWAREGLY G:22 , ASN G:23 , GLY G:24 , TRP G:26 , ASP G:57 , ASN G:60 , TRP G:61 , ILE G:62 , HOH G:108BINDING SITE FOR RESIDUE GDL G 110
09AC9SOFTWAREGLY I:22 , ASN I:23 , GLY I:24 , TRP I:26 , PHE I:29 , ASP I:57 , ASN I:60 , TRP I:61 , ILE I:62BINDING SITE FOR RESIDUE GDL I 110
10BC1SOFTWAREGLY J:22 , ASN J:23 , GLY J:24 , TRP J:26 , ASP J:57 , ASP J:59 , ASN J:60 , TRP J:61 , ILE J:62BINDING SITE FOR RESIDUE GDL J 110
11BC2SOFTWAREARG E:91 , ARG J:91 , GLY J:92 , GLN J:93 , ARG J:94BINDING SITE FOR RESIDUE SO4 J 107

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KIF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 10)

Asymmetric Unit (1, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TAL2_TACTR_001 *I148VTAL2_TACTR  ---  ---A/B/C/D/E/F/G/H/I/JI68V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TAL2_TACTR_001 *I148VTAL2_TACTR  ---  ---A/B/C/D/E/F/G/H/I/JI68V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TAL2_TACTR_001 *I148VTAL2_TACTR  ---  ---A/B/C/D/EI68V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TAL2_TACTR_001 *I148VTAL2_TACTR  ---  ---F/G/H/I/JI68V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KIF)

(-) 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:93
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:93
                                    99       109       119       129       139       149       159       169       179   
           TAL2_TACTR    90 DNDNWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPV 182
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhheeee........eeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------V---------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3kif A  10 DSDNWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPV 102
                                    19        29        39        49        59        69        79        89        99   

Chain B from PDB  Type:PROTEIN  Length:88
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:88
                                   103       113       123       133       143       153       163       173        
           TAL2_TACTR    94 WMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPP 181
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhh..eee.....eeeee..eeeee........hhhhhheeee......eeeeee.....eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------V--------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3kif B  14 WMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPP 101
                                    23        33        43        53        63        73        83        93        

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:85
                                   108       118       128       138       148       158       168       178     
           TAL2_TACTR    99 KKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVS 183
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhh.eeee.....eeeee..eeeee.........hhhhheeeee.hhhhh.eeee.....eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------V----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3kif C  19 KEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVS 103
                                    28        38        48        58        68        78        88        98     

Chain D from PDB  Type:PROTEIN  Length:91
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:91
                                   102       112       122       132       142       152       162       172       182 
           TAL2_TACTR    93 NWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVS 183
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhh.eeeeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------V----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3kif D  13 NWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVS 103
                                    22        32        42        52        62        72        82        92       102 

Chain E from PDB  Type:PROTEIN  Length:93
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:93
                                   102       112       122       132       142       152       162       172       182   
           TAL2_TACTR    93 NWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVSNQ 185
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeee..hhhhh.eeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------V------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3kif E  13 NWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVSNQ 105
                                    22        32        42        52        62        72        82        92       102   

Chain F from PDB  Type:PROTEIN  Length:92
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:92
                                   100       110       120       130       140       150       160       170       180  
           TAL2_TACTR    91 NDNWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPV 182
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhheeee........eeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------V---------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3kif F  11 SDNWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPV 102
                                    20        30        40        50        60        70        80        90       100  

Chain G from PDB  Type:PROTEIN  Length:88
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:88
                                   103       113       123       133       143       153       163       173        
           TAL2_TACTR    94 WMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPP 181
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee........eeee.....eeeee..eeeee........hhhhhheeee..hhh.eeeeee.....eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------V--------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3kif G  14 WMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPP 101
                                    23        33        43        53        63        73        83        93        

Chain H from PDB  Type:PROTEIN  Length:85
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:85
                                   108       118       128       138       148       158       168       178     
           TAL2_TACTR    99 KKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVS 183
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeee.....eeeee..eeeee.........hhhhheeee..hhhhh.eeee.....eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------V----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3kif H  19 KEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVS 103
                                    28        38        48        58        68        78        88        98     

Chain I from PDB  Type:PROTEIN  Length:94
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:94
                                    99       109       119       129       139       149       159       169       179    
           TAL2_TACTR    90 DNDNWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVS 183
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeee..hhhhh.eeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------V----------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3kif I  10 DSDNWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVS 103
                                    19        29        39        49        59        69        79        89        99    

Chain J from PDB  Type:PROTEIN  Length:93
 aligned with TAL2_TACTR | Q27084 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:93
                                   102       112       122       132       142       152       162       172       182   
           TAL2_TACTR    93 NWMGRAKKIGNGGWNQFQFLFFDPNGYLYAVSKDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVHGQQFYKALPPVSNQ 185
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeee..hhhhh.eeee.....eeeee..eeeee........hhhhhheeee..hhhhh.eeee.....eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------V------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3kif J  13 NWMGRAKEIGNGGWDQFQFLFFDPNGYLYAVSNDKLYKASPPQSDTDNWIARATEIGSGGWSGFKFLFFHPNGYLYAVRGQRFYKALPPVSNQ 105
                                    22        32        42        52        62        72        82        92       102   

   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 3KIF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (TAL2_TACTR | Q27084)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TAL2_TACTR | Q270841tl2 3kih

(-) Related Entries Specified in the PDB File

3kih