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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CANAVALIA MARITIMA LECTIN (CONM) IN COMPLEX WITH TREHALOSE AND MALTOSE
 
Authors :  P. Delatorre, B. A. M. Rocha, E. P. Sousa, C. A. A. Gadelha, W. F. Azevedo Jr. , B. S. Cavada
Date :  06 Jul 05  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Canacalia Maritima, Lectin, Maltose, Crystal Structure, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Delatorre, B. A. M. Rocha, C. A. A. Gadelha, T. Santi-Gadelha, J. B. Cajazeiras, E. P. Souza, K. S. Nascimento, V. N. Freire, A. H. Sampaio, W. F. Azevedo Jr. , B. S. Cavada
Crystal Structure Of A Lectin From Canavalia Maritima (Conm) In Complex With Trehalose And Maltose Reveals Relevant Mutation In Cona-Like Lectins
J. Struct. Biol. V. 154 280 2006
PubMed-ID: 16677825  |  Reference-DOI: 10.1016/J.JSB.2006.03.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN
    Chains: A, C
    Organism Scientific: CANAVALIA MARITIMA
    Organism Taxid: 3825
    Tissue: SEEDS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MAL2Ligand/IonMALTOSE
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAL4Ligand/IonMALTOSE
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:12 , ASN A:14 , PRO A:68 , ASN A:69 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228BINDING SITE FOR RESIDUE MAL A 240
2AC2SOFTWARETYR C:12 , ASN C:14 , PRO C:68 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , GLY C:227 , ARG C:228 , HOH C:495BINDING SITE FOR RESIDUE MAL C 1240
3AC3SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:479 , HOH A:562BINDING SITE FOR RESIDUE CA A 238
4AC4SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:500 , HOH C:520BINDING SITE FOR RESIDUE CA C 238
5AC5SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:524 , HOH C:566BINDING SITE FOR RESIDUE MN C 239
6AC6SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:483 , HOH A:551BINDING SITE FOR RESIDUE MN A 239

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CYF)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:149 -Thr A:150
2Ala A:207 -Asp A:208
3Gly C:149 -Thr C:150
4Ala C:207 -Asp C:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CYF)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANBR5-11
 		  2A:5-11
C:5-11
CONA_CANLI5-11  1A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANBR85-94
 		  2A:85-94
C:85-94
CONA_CANLI85-94  1A:85-94
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANBR5-11
 		  4A:5-11
C:5-11
CONA_CANLI5-11  2A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANBR85-94
 		  4A:85-94
C:85-94
CONA_CANLI85-94  2A:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 2CYF)

(-) 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:230
 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 d2cyfa_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cyfA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........ee.eeeeeeeee------.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeee-..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cyf A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLK------TNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTF-IKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110     |   -  |    130       140       150       160       170       180       190      |200       210       220       230       
                                                                                                                                             116    123                                                                       197 |                                      
                                                                                                                                                                                                                                199                                      


Chain A from PDB  Type:PROTEIN  Length:230
 aligned with CONA_CANLI | P81460 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_CANLI     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d2cyfa_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cyfA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........ee.eeeeeeeee------.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeee-..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cyf A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLK------TNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTF-IKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110     |   -  |    130       140       150       160       170       180       190      |200       210       220       230       
                                                                                                                                             116    123                                                                       197 |                                      
                                                                                                                                                                                                                                199                                      


Chain C from PDB  Type:PROTEIN  Length:231
 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 d2cyfc_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cyfC00 C:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee------.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cyf C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLK------TNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110     |   -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                             116    123
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CYF)

(-) Gene Ontology  (4, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CONA_CANLI | P81460)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

Chain A,C   (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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  2cyf
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  CONA_CANLI | P81460
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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 3ju9 4h55 4p14 4pcr
        CONA_CANLI | P81460: 2cwm 2cy6 3snm 4dpn 4i30 4tys 4tzd 5byn

(-) Related Entries Specified in the PDB File

2cwm NATIVE CRYSTAL STRUCTURE OF CONM
2cy6 CRYSTAL STRUCTURE OF CONM IN COMPLEX WITH TREHALOSE