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(-) Description

Title :  CRYSTAL STRUCTURE OF CONCANAVALIN A BOUND TO AN OCTA-ALPHA-MANNOSYL-OCTASILSESQUIOXANE CLUSTER
 
Authors :  E. J. Sundberg, D. A. Bonsor, B Trastoy, J. L. Chiara
Date :  03 Feb 11  (Deposition) - 08 Feb 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Concanavalin A-Like Lectins/Glucanases, Sugar Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Trastoy, D. A. Bonsor, M. E. Perez-Ojeda, E. J. Sundberg, M. L. Jimeno, J. M. Garcia-Fernandez, J. L. Chiara
Synthesis And Biophysical Study Of Disassembling Nano Hybri Bioconjugates With A Cubic Octasilsesquioxane Core
Adv Funct Mater V. 22 3191 2012
PubMed: search  |  Reference-DOI: 10.1002/ADFM.201200423

(-) Compounds

Molecule 1 - CONCANAVALIN-A
    Chains: A, B, C, D
    Organism Common: JACKBEAN
    Organism Scientific: CANAVALIA CATHARTICA
    Organism Taxid: 28958
    Synonym: CON A

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MAN4Ligand/IonALPHA-D-MANNOSE
3MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:275 , HOH A:281BINDING SITE FOR RESIDUE CA A 238
02AC2SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:259 , HOH A:262 , HOH A:297BINDING SITE FOR RESIDUE MN A 239
03AC3SOFTWARETYR 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:270BINDING SITE FOR RESIDUE MAN A 240
04AC4SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:259 , HOH B:283BINDING SITE FOR RESIDUE MN B 238
05AC5SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:258 , HOH B:276BINDING SITE FOR RESIDUE CA B 239
06AC6SOFTWAREASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , HOH B:272BINDING SITE FOR RESIDUE MAN B 240
07AC7SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:255 , HOH C:297BINDING SITE FOR RESIDUE MN C 238
08AC8SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:262 , HOH C:298BINDING SITE FOR RESIDUE CA C 239
09AC9SOFTWARETYR 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:228BINDING SITE FOR RESIDUE MAN C 240
10BC1SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:253 , HOH D:266BINDING SITE FOR RESIDUE CA D 238
11BC2SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:251 , HOH D:286BINDING SITE FOR RESIDUE MN D 239
12BC3SOFTWAREASN 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:273BINDING SITE FOR RESIDUE MAN D 240

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.CONA_CANCT5-11
 
 
 		  4A:5-11
B:5-11
C:5-11
D:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.CONA_CANCT85-94
 
 
 		  4A:85-94
B:85-94
C:85-94
D:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 3QLQ)

(-) 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:236
 aligned with CONA_CANCT | P81461 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_CANCT     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d3qlqa_ A: Concanavalin A                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee...-.eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qlq A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNST-ETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                 120 |                                                                                                                   
                                                                                                                                                   122                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with CONA_CANCT | P81461 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_CANCT     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d3qlqb_ B: Concanavalin A                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee..--.eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qlq B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNS--ETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110        |- |     130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                119  |                                                                                                                   
                                                                                                                                                   122                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:236
 aligned with CONA_CANCT | P81461 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_CANCT     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d3qlqc_ C: Concanavalin A                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee...-.eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qlq C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNST-ETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                 120 |                                                                                                                   
                                                                                                                                                   122                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:232
 aligned with CONA_CANCT | P81461 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_CANCT     1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
               SCOP domains d3qlqd_ D: Concanavalin A                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.-----.eeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qlq D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKS-----TNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110      |  -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                              117   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QLQ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CONA_CANCT | P81461)
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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    Ala A:207 - Asp A:208   [ RasMol ]  
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    Ala D:207 - Asp D:208   [ RasMol ]  
 

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  3qlq
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 Related Entries

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

UniProtKB/Swiss-Prot
        CONA_CANCT | P81461: 1hqw 1qgl 2a7a 2g4i 4czs 5f5q

(-) Related Entries Specified in the PDB File

1scr CONCANAVALIN A
3d4k CONCANAVALIN A COMPLEXED TO A SYNTHETIC ANALOG OF THE TRIMANNOSIDE