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(-) Description

Title :  CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED LECTIN COMPLEXED WITH LACTOSE
 
Authors :  B. L. Sousa, J. C. Silva-Filho, P. Kumar, A. Lyskowski, G. A. Bezerra, P. Delatorre, B. A. M. Rocha, R. M. S. Cunha, C. S. Nagano, K. Gruber, B. S
Date :  04 Nov 14  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Recombinant, Lectin, Legume, Dalbergieae, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Sousa, J. C. Silva-Filho, P. Kumar, M. A. Graewert, R. I. Pereira, R. M. Cunha, K. S. Nascimento, G. A. Bezerra, P. Delatorre, K. Djinovic-Carugo, C. S. Nagano, K. Gruber, B. S. Cavada
Structural Characterization Of A Vatairea Macrocarpa Lectin In Complex With A Tumor-Associated Antigen: A New Tool For Cancer Research.
Int. J. Biochem. Cell Biol. V. 72 27 2016
PubMed-ID: 26751394  |  Reference-DOI: 10.1016/J.BIOCEL.2015.12.016

(-) Compounds

Molecule 1 - SEED LECTIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Taxid: 469008
    Expression System Variant: CODON-PLUS
    Expression System Vector Type: PLASMID
    Organism Scientific: VATAIREA MACROCARPA
    Organism Taxid: 77050
    Synonym: VML

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2LBT4Ligand/IonALPHA-LACTOSE
3MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:126 , PHE A:128 , ASN A:130 , ASP A:133 , HOH A:460 , HOH A:468binding site for residue CA A 301
02AC2SOFTWAREGLU A:124 , ASP A:126 , ASP A:133 , HIS A:138 , HOH A:452 , HOH A:454binding site for residue MN A 302
03AC3SOFTWAREASP A:45 , HIS A:46 , ALA A:87 , ASP A:88 , GLY A:106 , PHE A:128 , ASN A:130 , GLY A:213 , LEU A:214 , SER A:215 , ARG A:216 , HIS A:218 , HOH A:406 , HOH A:407 , HOH A:410 , HOH A:413 , HOH A:442 , HOH A:515 , HOH A:533binding site for residue LBT A 303
04AC4SOFTWAREASP B:126 , PHE B:128 , ASN B:130 , ASP B:133 , HOH B:441 , HOH B:475binding site for residue CA B 301
05AC5SOFTWAREGLU B:124 , ASP B:126 , ASP B:133 , HIS B:138 , HOH B:467 , HOH B:485binding site for residue MN B 302
06AC6SOFTWAREASP B:88 , GLY B:106 , ASN B:130 , GLY B:213 , LEU B:214 , SER B:215 , HIS B:218 , HOH B:458 , HOH B:483 , HOH B:498 , HOH B:566binding site for residue LBT B 303
07AC7SOFTWAREASP C:126 , PHE C:128 , ASN C:130 , ASP C:133 , HOH C:458 , HOH C:471binding site for residue CA C 301
08AC8SOFTWAREGLU C:124 , ASP C:126 , ASP C:133 , HIS C:138 , HOH C:427 , HOH C:434binding site for residue MN C 302
09AC9SOFTWAREASP C:88 , GLY C:106 , PHE C:128 , ASN C:130 , GLY C:213 , LEU C:214 , SER C:215 , HIS C:218 , HOH C:431 , HOH C:491binding site for residue LBT C 303
10AD1SOFTWAREASP D:126 , PHE D:128 , ASN D:130 , ASP D:133 , HOH D:415 , HOH D:493binding site for residue CA D 301
11AD2SOFTWAREGLU D:124 , ASP D:126 , ASP D:133 , HIS D:138 , HOH D:422 , HOH D:434binding site for residue MN D 302
12AD3SOFTWAREALA D:87 , ASP D:88 , GLY D:106 , PHE D:128 , ASN D:130 , GLY D:213 , LEU D:214 , SER D:215 , HIS D:218 , HOH D:408 , HOH D:428 , HOH D:453binding site for residue LBT D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WV8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:87 -Asp A:88
2Ala B:87 -Asp B:88
3Ala C:87 -Asp C:88
4Ala D:87 -Asp D:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WV8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WV8)

(-) Exons   (0, 0)

(no "Exon" information available for 4WV8)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.eehhhhee.eeeeeeeee..........eeeeeeee........hhhhh............eeeeee...........eeeeee......eeee........eeeeeeeehhh.eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wv8 A   1 MSEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSNKSIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAP 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.eehhhhee.eeeeeeeee..........eeeeeeee........hhhhh............eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........ee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wv8 B   1 MSEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSNKSIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAPS 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee........eeeeeeeeeee..........eeeeeeee........hhhhh.........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wv8 C   1 MSEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAPSDDSN 241
                                    10        20        30        40        50        60        70        80        90       100       110   ||  123       133       143       153       163       173       183       193       203       213       223       233        
                                                                                                                                           114|                                                                                                                           
                                                                                                                                            118                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee..........eeeeeeee........hhhhh..........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wv8 D   1 MSEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSSIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAPSDDSN 241
                                    10        20        30        40        50        60        70        80        90       100       110   ||  122       132       142       152       162       172       182       192       202       212       222       232         
                                                                                                                                           114|                                                                                                                            
                                                                                                                                            117
   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 4WV8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WV8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WV8)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:87 - Asp A:88   [ RasMol ]  
    Ala B:87 - Asp B:88   [ RasMol ]  
    Ala C:87 - Asp C:88   [ RasMol ]  
    Ala D:87 - Asp D:88   [ RasMol ]  
 

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 Related Entries

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        LECS_VATMA | P81371: 4u2a 4u36 4xtm 4xtp 4xxa

(-) Related Entries Specified in the PDB File

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