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(-) Description

Title :  CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA BRASILIENSIS SEED (CONBR) COMPLEXED WITH ALPHA-AMINOBUTYRIC ACID
 
Authors :  E. H. S. Bezerra, B. A. M. Rocha, C. S. Nagano, G. A. Bezerra, T. R. Moura, M. J. B. Bezerra, R. G. Benevides, E. S. Marinho, P. Delatorre, B. S. Cav
Date :  14 Sep 09  (Deposition) - 08 Dec 10  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Conbr, Lectin, Agglutinin, Canavalia Brasiliensis, Manganese, Metal- Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Bezerra, B. A. Rocha, C. S. Nagano, G. A. Bezerra, T. R. Moura, M. J. Bezerra, R. G. Benevides, A. H. Sampaio, A. M. Assreuy, P. Delatorre, B. S. Cavada
Structural Analysis Of Conbr Reveals Molecular Correlation Between The Carbohydrate Recognition Domain And Endothelial No Synthase Activation.
Biochem. Biophys. Res. Commun. V. 408 566 2011
PubMed-ID: 21530490  |  Reference-DOI: 10.1016/J.BBRC.2011.04.061

(-) Compounds

Molecule 1 - CONCANAVALIN-BR
    Chains: A
    Organism Common: BRAZILIAN JACK BEAN
    Organism Scientific: CANAVALIA BRASILIENSIS
    Organism Taxid: 61861
    Synonym: CON BR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3DBB1Ligand/IonD-ALPHA-AMINOBUTYRIC ACID
4GOL1Ligand/IonGLYCEROL
5MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DBB4Ligand/IonD-ALPHA-AMINOBUTYRIC ACID
4GOL4Ligand/IonGLYCEROL
5MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:113 , ASN A:124 , ALA A:125 , MET A:129 , PHE A:130 , ASP A:139 , VAL A:179 , HIS A:180 , HOH A:254 , HOH A:271BINDING SITE FOR RESIDUE DBB A 238
2AC2SOFTWARETYR A:12 , ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , ARG A:228BINDING SITE FOR RESIDUE GOL A 239
3AC3SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:244 , HOH A:245BINDING SITE FOR RESIDUE CA A 240
4AC4SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:246 , HOH A:260BINDING SITE FOR RESIDUE MN A 241
5AC5SOFTWAREALA A:236BINDING SITE FOR RESIDUE CL A 242
6AC6SOFTWAREASN A:14 , ARG A:228 , HOH A:382BINDING SITE FOR RESIDUE CL A 243

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JU9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:207 -Asp A:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JU9)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANBR5-11  1A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANBR85-94  1A:85-94
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANBR5-11  4A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANBR85-94  4A:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 3JU9)

(-) 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:237
 aligned with CONA_CANBR | P55915 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           CONA_CANBR     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTEGNLRLTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d3ju9a_ A: Concanavalin A                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-3ju9A01 A:124-237                                                                                      Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-3ju9A02 A:124-237                                                                                      Pfam domains (2)
         Sec.struct. author ...eeeeeee.............eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.......eeeeeeeeeeee.......eeeeeee.........eeeee..ee.....ee.............eeeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ju9 A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTEGNLRLTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JU9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (CONA_CANBR | P55915)
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.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  CONA_CANBR | P55915
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 Related Entries

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

UniProtKB/Swiss-Prot
        CONA_CANBR | P55915: 1azd 1c57 1dq0 1dq1 1dq2 1dq4 1dq5 1joj 1jui 1jyc 1jyi 1qdc 1qdo 2cyf 4h55 4p14 4pcr

(-) Related Entries Specified in the PDB File

1azd