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(-) Description

Title :  CRYSTAL STRUCTURE OF CANAVALIA BOLIVIANA LECTIN IN COMPLEX WITH MAN1-4MAN-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 :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Diocleinae Lectins, Dimannosides, Oligomerization, Binding Sites, Jelly Roll, Carbohydrate Binding, 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  (6, 27)

Asymmetric/Biological Unit (6, 27)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CD9Ligand/IonCADMIUM ION
3CL2Ligand/IonCHLORIDE ION
4MAN4Ligand/IonALPHA-D-MANNOSE
5MMA4Ligand/IonO1-METHYL-MANNOSE
6MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:405 , HOH A:411BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:401 , HOH A:402BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWARELYS A:30 , HOH A:494 , ASN D:83BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWARELEU A:107 , ASN A:131 , GLY A:152 , ASN A:153 , HOH A:490 , GLU B:122BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWAREASP A:80 , ASP A:82 , HOH A:455 , HOH A:458 , HOH A:482 , HOH A:492BINDING SITE FOR RESIDUE CD A 305
06AC6SOFTWAREASP A:82 , TRP A:182 , HOH A:484 , HOH A:542BINDING SITE FOR RESIDUE CD A 306
07AC7SOFTWARETYR A:12 , LEU A:99 , MAN A:308BINDING SITE FOR RESIDUE MMA A 307
08AC8SOFTWAREASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228 , MMA A:307 , HOH A:448 , HOH A:491BINDING SITE FOR RESIDUE MAN A 308
09AC9SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:402 , HOH B:419BINDING SITE FOR RESIDUE MN B 301
10BC1SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:403 , HOH B:405BINDING SITE FOR RESIDUE CA B 302
11BC2SOFTWAREHOH A:498 , LEU B:107 , ASN B:131 , GLY B:152 , ASN B:153BINDING SITE FOR RESIDUE CD B 303
12BC3SOFTWARETYR B:77 , ASP B:80 , ASP B:82 , HOH B:456 , HOH B:506BINDING SITE FOR RESIDUE CD B 304
13BC4SOFTWAREASP B:80 , ASN B:83BINDING SITE FOR RESIDUE CL B 305
14BC5SOFTWAREASN B:55 , HOH B:407 , ASN D:55 , GLY D:58 , HOH D:411BINDING SITE FOR RESIDUE CL B 306
15BC6SOFTWARETYR B:12 , MAN B:308BINDING SITE FOR RESIDUE MMA B 307
16BC7SOFTWAREASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , MMA B:307 , HOH B:440 , HOH B:475BINDING SITE FOR RESIDUE MAN B 308
17BC8SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:401 , HOH C:408BINDING SITE FOR RESIDUE MN C 301
18BC9SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:403 , HOH C:409BINDING SITE FOR RESIDUE CA C 302
19CC1SOFTWARELEU C:107 , ASN C:131 , GLY C:152 , ASN C:153 , HOH D:536BINDING SITE FOR RESIDUE CD C 303
20CC2SOFTWARETYR C:12 , MAN C:305BINDING SITE FOR RESIDUE MMA C 304
21CC3SOFTWAREASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , GLY C:227 , ARG C:228 , MMA C:304 , HOH C:425 , HOH C:445BINDING SITE FOR RESIDUE MAN C 305
22CC4SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:407 , HOH D:412BINDING SITE FOR RESIDUE MN D 301
23CC5SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:414 , HOH D:424BINDING SITE FOR RESIDUE CA D 302
24CC6SOFTWAREGLU C:122 , LEU D:107 , ASN D:131 , GLY D:152 , ASN D:153BINDING SITE FOR RESIDUE CD D 303
25CC7SOFTWAREASP D:80 , ASP D:82 , HOH D:509 , HOH D:514 , HOH D:525BINDING SITE FOR RESIDUE CD D 304
26CC8SOFTWARETYR D:12 , LEU D:99 , TYR D:100 , MAN D:306 , HOH D:521BINDING SITE FOR RESIDUE MMA D 305
27CC9SOFTWARETYR 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 , MMA D:305 , HOH D:431 , HOH D:458BINDING SITE FOR RESIDUE MAN D 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K1Z)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ala A:207 -Asp A:208
2Ala B:207 -Asp B:208
3Ala C:207 -Asp C:208
4Asn D:69 -Gly D:70
5Ala D:207 -Asp D:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4K1Z)

(-) 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 d4k1za_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1z 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 d4k1zb_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1z 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 d4k1zc_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeee.....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1z 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 d4k1zd_ D: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1z 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)
  - → 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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K1Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K1Z)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4K1Z)

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  Cis Peptide Bonds
    Ala A:207 - Asp A:208   [ RasMol ]  
    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: 4k1y 4k20 4k21

(-) Related Entries Specified in the PDB File

4k1y 4k20 4k21