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(-) Description

Title :  CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA MARITIMA SEEDS (CML) IN COMPLEX WITH MAN1-4MAN-OME
 
Authors :  F. B. M. B. Moreno, G. A. Bezerra, T. M. Oliveira, E. P. Souza, B. A. M. Rocha, R. G. Benevides, P. Delatorre, B. S. Cavada, W. De Azevedo Jr.
Date :  08 Mar 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,O#,P#,Q#,R#
Biol. Unit 1:  A,B,C,D  (1x)
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Canavalia Maritima Lectin, Dimannoside, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. A. Bezerra, T. M. Oliveira, F. B. M. B. Moreno, E. P. De Souza, B. A. M. Da Rocha, R. G. Benevides, P. Delatorre, W. F. De Azevedo Jr. , B. S. Cavada
Structural Analysis Of Canavalia Maritima And Canavalia Gladiata Lectins Complexed With Different Dimannosides: New Insights Into The Understanding Of The Structure-Biological Activity Relationship In Legume Lectins.
J. Struct. Biol. V. 160 168 2007
PubMed-ID: 17881248  |  Reference-DOI: 10.1016/J.JSB.2007.07.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN
    ChainsA, B, C, D
    Organism ScientificCANAVALIA MARITIMA
    Organism Taxid3825
    Other DetailsSEED PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDO#P#Q#R#
Biological Unit 1 (1x)ABCD    
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MAN4Ligand/IonALPHA-D-MANNOSE
3MMA4Ligand/IonO1-METHYL-MANNOSE
4MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAN-1Ligand/IonALPHA-D-MANNOSE
3MMA-1Ligand/IonO1-METHYL-MANNOSE
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU D:99 , MAN O:1BINDING SITE FOR RESIDUE MMA O 2
02AC2SOFTWARETYR 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 O:2BINDING SITE FOR RESIDUE MAN O 1
03AC3SOFTWARETYR A:12 , VAL B:57 , GLY B:58 , ASP B:78 , ARG D:60 , THR D:74 , SER D:76 , HOH D:312 , MAN P:1 , HOH P:3BINDING SITE FOR RESIDUE MMA P 2
04AC4SOFTWARETYR 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 B:368 , MMA P:2 , HOH P:4BINDING SITE FOR RESIDUE MAN P 1
05AC5SOFTWAREVAL A:57 , GLY A:58 , ASP A:78 , LEU B:99 , ARG C:60 , THR C:74 , SER C:76 , MAN Q:1 , HOH Q:3BINDING SITE FOR RESIDUE MMA Q 2
06AC6SOFTWAREHOH A:345 , TYR 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:228 , MMA Q:2 , HOH Q:4BINDING SITE FOR RESIDUE MAN Q 1
07AC7SOFTWARELEU C:99 , PRO D:68 , MAN R:1BINDING SITE FOR RESIDUE MMA R 2
08AC8SOFTWARETYR 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 , MMA R:2BINDING SITE FOR RESIDUE MAN R 1
09AC9SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:328 , HOH A:350BINDING SITE FOR RESIDUE MN A 238
10BC1SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:245 , HOH A:253BINDING SITE FOR RESIDUE CA A 239
11BC2SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:290 , HOH B:343BINDING SITE FOR RESIDUE MN B 238
12BC3SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:242 , HOH B:250BINDING SITE FOR RESIDUE CA B 239
13BC4SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:266 , HOH C:313BINDING SITE FOR RESIDUE MN C 238
14BC5SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:242 , HOH C:270BINDING SITE FOR RESIDUE CA C 239
15BC6SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:268BINDING SITE FOR RESIDUE MN D 238
16BC7SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:240 , HOH D:276BINDING SITE FOR RESIDUE CA D 239

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P34)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:149 -Thr A:150
2Ala A:207 -Asp A:208
3Lys B:116 -Ser B:117
4Ser B:117 -Asn B:118
5Ala B:207 -Asp B:208
6Gly C:149 -Thr C:150
7Ala C:207 -Asp C:208
8Ser D:117 -Asn D:118
9Gly D:149 -Thr D:150
10Thr D:150 -Asp D:151
11Ala D:207 -Asp D:208
12Leu D:229 -Leu D:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P34)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANRO5-11
 
 
 
  4A:5-11
B:5-11
C:5-11
D:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANRO84-93
 
 
 
  4A:85-94
B:85-94
C:85-94
D:85-94
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANRO5-11
 
 
 
  4A:5-11
B:5-11
C:5-11
D:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANRO84-93
 
 
 
  4A:85-94
B:85-94
C:85-94
D:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 2P34)

(-) 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
 aligned with CONA_CANRO | P81364 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:237
                                                               36                                                                                                                                                                                                        
                                                             35 |                                                                                                                                                                                                        
                                    10        20        30    | | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
           CONA_CANRO     1 ADTIVAVELDTYPNTDVGDPSYPHXXXXXXSVRXX-TAKWNMQNGKVGTAHISYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFTKDQKDLILQSDATTGTDGNLXXTRVSSNGPSQGSTVGRALFYAPVHIWESSATVAGFDATFXXLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 236
               SCOP domains d2p34a_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2p34A00 A: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......eeeeeeeeeeeeee...---.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeeeee........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p34 A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNS---TNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110        |-  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                119 123                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANRO | P81364 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:237
                                                               36                                                                                                                                                                                                        
                                                             35 |                                                                                                                                                                                                        
                                    10        20        30    | | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
           CONA_CANRO     1 ADTIVAVELDTYPNTDVGDPSYPHXXXXXXSVRXX-TAKWNMQNGKVGTAHISYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFTKDQKDLILQSDATTGTDGNLXXTRVSSNGPSQGSTVGRALFYAPVHIWESSATVAGFDATFXXLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 236
               SCOP domains d2p34b_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2p34B00 B: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 ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p34 B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSN---ETNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       | - |     130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                               118 122                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANRO | P81364 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:237
                                                               36                                                                                                                                                                                                        
                                                             35 |                                                                                                                                                                                                        
                                    10        20        30    | | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
           CONA_CANRO     1 ADTIVAVELDTYPNTDVGDPSYPHXXXXXXSVRXX-TAKWNMQNGKVGTAHISYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFTKDQKDLILQSDATTGTDGNLXXTRVSSNGPSQGSTVGRALFYAPVHIWESSATVAGFDATFXXLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 236
               SCOP domains d2p34c_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2p34C00 C:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee......eeeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee...---eeeeeeee.........eeeee..ee.....ee...ee...ee....eeeeee...ee.......eeeeeeeeeeee.........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p34 C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNS---TNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110        |-  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                119 123                                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANRO | P81364 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:237
                                                               36                                                                                                                                                                                                        
                                                             35 |                                                                                                                                                                                                        
                                    10        20        30    | | 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
           CONA_CANRO     1 ADTIVAVELDTYPNTDVGDPSYPHXXXXXXSVRXX-TAKWNMQNGKVGTAHISYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFTKDQKDLILQSDATTGTDGNLXXTRVSSNGPSQGSTVGRALFYAPVHIWESSATVAGFDATFXXLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 236
               SCOP domains d2p34d_ D: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2p34D00 D:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D01 D:124-237                                                                                      Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D02 D:124-237                                                                                      Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D03 D:124-237                                                                                      Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D04 D:124-237                                                                                      Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D05 D:124-237                                                                                      Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D06 D:124-237                                                                                      Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D07 D:124-237                                                                                      Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p34D08 D:124-237                                                                                      Pfam domains (8)
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee..---.eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p34 D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSN---ETNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       | - |     130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                               118 122                                                                                                                   

   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 Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 8)

Asymmetric Unit

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CONA_CANRO | P81364)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        CONA_CANRO | P813642cwm 2ow4 2p37

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P34)