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(-) Description

Title :  CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED LECTIN
 
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 :  30 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Legume, Recombinant Lectin, Vatairea, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  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. Cavada
Crystal Structure Of A Recombinant Vatairea Macrocarpa Seed Lectin
Int. J. Biochem. Cell Biol. 2016
PubMed: search

(-) Compounds

Molecule 1 - SEED LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organ: SEED
    Organism Scientific: VATAIREA MACROCARPA
    Organism Taxid: 77050
    Synonym: VML

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CA2Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:126 , PHE A:128 , ASN A:130 , ASP A:133 , HOH A:429 , HOH A:433binding site for residue CA A 301
2AC2SOFTWAREGLU A:124 , ASP A:126 , ASP A:133 , HIS A:138 , HOH A:437 , HOH A:465binding site for residue MN A 302
3AC3SOFTWAREASP A:88 , GLY A:106 , PHE A:128 , ASN A:130 , GLY A:213 , LEU A:214 , SER A:215binding site for residue GOL A 303
4AC4SOFTWAREHIS A:46 , ASP A:104 , LEU A:214 , HOH A:405 , 1PE B:304binding site for residue 1PE A 304
5AC5SOFTWAREASP B:126 , PHE B:128 , ASN B:130 , ASP B:133 , HOH B:427 , HOH B:442binding site for residue CA B 301
6AC6SOFTWAREGLU B:124 , ASP B:126 , ASP B:133 , HIS B:138 , HOH B:426 , HOH B:472binding site for residue MN B 302
7AC7SOFTWAREASP B:88 , GLY B:106 , ASP B:113 , PHE B:128 , ASN B:130 , GLY B:213 , LEU B:214 , HOH B:401binding site for residue GOL B 303
8AC8SOFTWARE1PE A:304 , HOH A:405 , GLU B:79 , ASN B:158 , HOH B:486binding site for residue 1PE B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:87 -Asp A:88
2Ala B:87 -Asp B:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XXA)

(-) 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:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.eehhhheeeeeeeeeeee..........eeeeeeee........hhhhh...........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xxa A   2 SEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDNKSIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAP 236
                                    11        21        31        41        51        61        71        81        91       101       111 ||    122       132       142       152       162       172       182       192       202       212       222       232    
                                                                                                                                         113|                                                                                                                         
                                                                                                                                          115                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.ee....ee.eeeeeeeee..........eeeeeeee........hhhhh..........eeeeee...........eeeeee......eeee........eeeeeeeehhh.eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xxa B   1 ASEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSNIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAP 236
                                    10        20        30        40        50        60        70        80        90       100       110    || 122       132       142       152       162       172       182       192       202       212       222       232    
                                                                                                                                            115|                                                                                                                      
                                                                                                                                             118
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  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 4XXA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:87 - Asp A:88   [ RasMol ]  
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  4xxa
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  LECS_VATMA | P81371
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECS_VATMA | P81371: 4u2a 4u36 4wv8 4xtm 4xtp

(-) Related Entries Specified in the PDB File

4wv8 CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED LECTIN COMPLEXED WITH LACTOSE
4xtm
4xtp