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(-) Description

Title :  CRYSTAL STRUCTURE OF CANAVALIA BOLIVIANA LECTIN IN COMPLEX WITH MAN1-3MAN-OME
 
Authors :  G. A. Bezerra, R. Viertlmayr, T. R. Moura, P. Delatorre, B. A. M. Rocha, B. S. Cavada, K. Gruber
Date :  07 Apr 13  (Deposition) - 09 Apr 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Diocleinae Lectins, Dimannosides, Oligomerization, Binding Sites, Mannose Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. A. Bezerra, R. Viertlmayr, T. R. Moura, P. Delatorre, B. A. Rocha, K. S. Do Nascimento, J. G. Figueiredo, I. G. Bezerra, C. S. Teixeira, R. C. Simoes, C. S. Nagano, N. M. De Alencar, K. Gruber, B. S. Cavada
Structural Studies Of An Anti-Inflammatory Lectin From Canavalia Boliviana Seeds In Complex With Dimannosides.
Plos One V. 9 97015 2014
PubMed-ID: 24865454  |  Reference-DOI: 10.1371/JOURNAL.PONE.0097015

(-) Compounds

Molecule 1 - CANAVALIA BOLIVIANA LECTIN
    Chains: A, B, C, D
    Organism Scientific: CANAVALIA BOLIVIANA
    Organism Taxid: 232300
    Other Details: SEEDS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CD9Ligand/IonCADMIUM ION
3MDM4Ligand/IonMETHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE
4MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:417BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:422BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREASP A:80 , ASP A:82 , HOH A:430 , HOH A:431 , SER B:160BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWAREASP A:235BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWARETYR A:12 , ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228 , HOH A:446 , HOH A:447BINDING SITE FOR RESIDUE MDM A 305
06AC6SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:408BINDING SITE FOR RESIDUE MN B 301
07AC7SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:402BINDING SITE FOR RESIDUE CA B 302
08AC8SOFTWAREASP B:80 , ASP B:82 , HOH B:427 , HOH B:441 , LYS C:135BINDING SITE FOR RESIDUE CD B 303
09AC9SOFTWAREASP B:235BINDING SITE FOR RESIDUE CD B 304
10BC1SOFTWARETYR B:12 , ASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228BINDING SITE FOR RESIDUE MDM B 305
11BC2SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:405BINDING SITE FOR RESIDUE MN C 301
12BC3SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:411 , HOH C:455BINDING SITE FOR RESIDUE CA C 302
13BC4SOFTWARELYS C:59 , ASP C:80 , ASP C:82 , LYS D:135BINDING SITE FOR RESIDUE CD C 303
14BC5SOFTWAREASP C:235 , HOH C:434 , HOH C:435BINDING SITE FOR RESIDUE CD C 304
15BC6SOFTWAREGLU C:87 , GLU C:183 , HOH C:449 , HOH C:450BINDING SITE FOR RESIDUE CD C 305
16BC7SOFTWARETYR C:12 , ASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , GLY C:227 , ARG C:228 , HOH C:425BINDING SITE FOR RESIDUE MDM C 306
17BC8SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:432BINDING SITE FOR RESIDUE MN D 301
18BC9SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:402BINDING SITE FOR RESIDUE CA D 302
19CC1SOFTWARELYS D:59 , ASP D:80 , ASP D:82 , HOH D:423 , HOH D:424BINDING SITE FOR RESIDUE CD D 303
20CC2SOFTWAREASP D:235 , ASN D:237BINDING SITE FOR RESIDUE CD D 304
21CC3SOFTWARETYR D:12 , ASN D:14 , GLY D:98 , LEU D:99 , TYR D:100 , ALA D:207 , ASP D:208 , GLY D:227 , ARG D:228 , HOH D:440BINDING SITE FOR RESIDUE MDM D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K1Y)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Thr A:120 -His A:121
2His A:121 -Glu A:122
3Ala A:207 -Asp A:208
4Thr B:120 -His B:121
5His B:121 -Glu B:122
6Ala B:207 -Asp B:208
7Ala C:207 -Asp C:208
8Asn D:69 -Gly D:70
9Thr D:120 -His D:121
10His D:121 -Glu D:122
11Ala D:207 -Asp D:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4K1Y)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4k1ya_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.............eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeeeee........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1y A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGRDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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 B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4k1yb_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.............eeeeee......eeee.......eeeeeeeee....eeeeeeee..eeeeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee.............eeeeeee...ee.....eeeeeeeeeeeeeee........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1y B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGRDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4k1yc_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.............eeeeee......eeee.......eeeeeeee.....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.....ee.............eeeeeee...ee.....eeeeeeeeeeeeeee........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1y C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGRDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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 D from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4k1yd_ D: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.............eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee.............eeeeeee...ee.....eeeeeeeeeeeeeee........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1y D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGRDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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)
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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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K1Y)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4K1Y)

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  Cis Peptide Bonds
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    Ala B:207 - Asp B:208   [ RasMol ]  
    Ala C:207 - Asp C:208   [ RasMol ]  
    Ala D:207 - Asp D:208   [ RasMol ]  
    Asn D:69 - Gly D:70   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_CANBL | A0A023GPI8: 4k1z 4k20 4k21

(-) Related Entries Specified in the PDB File

4k1z 4k20 4k21