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(-) Description

Title :  CONCANAVALIN A COMPLEXED TO A SYNTHETIC ANALOG OF THE TRIMANNOSIDE
 
Authors :  R. Kadirvelraj, B. L. Foley, J. D. Dyekjaer, R. J. Woods
Date :  14 May 08  (Deposition) - 03 Mar 09  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Concanavalin A, Conserved Water, Carbohydrate-Protein Binding, Glycoprotein, Lectin, Manganese, Metal-Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kadirvelraj, B. L. Foley, J. D. Dyekjaer, R. J. Woods
Involvement Of Water In Carbohydrate-Protein Binding: Concanavalin A Revisited.
J. Am. Chem. Soc. V. 130 16933 2008
PubMed-ID: 19053475  |  Reference-DOI: 10.1021/JA8039663
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONCANAVALIN-A
    Chains: A, B, C, D
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Other Details: JACK-BEAN
    Synonym: CON A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3H1M4Ligand/IonMETHYL 2-DEOXY-2-(2-HYDROXYETHYL)-ALPHA-D-MANNOPYRANOSIDE
4MAN8Ligand/IonALPHA-D-MANNOSE
5MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3H1M2Ligand/IonMETHYL 2-DEOXY-2-(2-HYDROXYETHYL)-ALPHA-D-MANNOPYRANOSIDE
4MAN4Ligand/IonALPHA-D-MANNOSE
5MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , ARG A:228 , HOH A:368 , HOH A:765BINDING SITE FOR RESIDUE MAN A 240
02AC2SOFTWARETYR A:12 , PRO A:13 , ASN A:14 , THR A:15 , ASP A:16BINDING SITE FOR RESIDUE MAN A 242
03AC3SOFTWARETYR 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 , HOH B:280 , HOH B:367BINDING SITE FOR RESIDUE MAN B 240
04AC4SOFTWARETYR B:12 , PRO B:13 , ASN B:14 , THR B:15 , ASP B:16 , HOH B:720BINDING SITE FOR RESIDUE MAN B 242
05AC5SOFTWAREASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , ARG C:228 , HOH C:370 , HOH C:371 , HOH C:742BINDING SITE FOR RESIDUE MAN C 240
06AC6SOFTWARETYR C:12 , PRO C:13 , ASN C:14 , THR C:15 , ASP C:16BINDING SITE FOR RESIDUE MAN C 242
07AC7SOFTWARETYR D:12 , ASN D:14 , GLY D:98 , LEU D:99 , TYR D:100 , ALA D:207 , ASP D:208 , ARG D:228 , HOH D:290 , HOH D:312BINDING SITE FOR RESIDUE MAN D 240
08AC8SOFTWARETYR D:12 , PRO D:13 , ASN D:14 , THR D:15 , ASP D:16BINDING SITE FOR RESIDUE MAN D 242
09AC9SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:307 , HOH A:365BINDING SITE FOR RESIDUE MN A 238
10BC1SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:250 , HOH A:447BINDING SITE FOR RESIDUE CA A 239
11BC2SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:264 , HOH B:306BINDING SITE FOR RESIDUE MN B 238
12BC3SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:257 , HOH B:444BINDING SITE FOR RESIDUE CA B 239
13BC4SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:256 , HOH C:386BINDING SITE FOR RESIDUE MN C 238
14BC5SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:281 , HOH C:449BINDING SITE FOR RESIDUE CA C 239
15BC6SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:270 , HOH D:271BINDING SITE FOR RESIDUE MN D 238
16BC7SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:253 , HOH D:445BINDING SITE FOR RESIDUE CA D 239
17BC8SOFTWARETYR A:12 , ASP A:16 , LEU A:99 , TYR A:100 , ARG A:228 , HOH A:390 , HOH A:759BINDING SITE FOR RESIDUE H1M A 241
18BC9SOFTWARETYR B:12 , ASP B:16 , ARG B:228 , HOH B:279 , HOH B:423BINDING SITE FOR RESIDUE H1M B 241
19CC1SOFTWARETYR C:12 , ASP C:16 , LEU C:99 , ARG C:228 , HOH C:448BINDING SITE FOR RESIDUE H1M C 241
20CC2SOFTWARETYR D:12 , ASP D:16 , LEU D:99 , ARG D:228 , HOH D:297 , HOH D:315 , HOH D:580BINDING SITE FOR RESIDUE H1M D 241
21CC3SOFTWAREPHE A:130 , ASP A:139 , HOH A:330 , SER D:113 , HIS D:180 , HOH D:509BINDING SITE FOR RESIDUE GOL D 900
22CC4SOFTWAREASP B:139 , HOH B:291 , SER C:113 , HIS C:180 , HOH C:717BINDING SITE FOR RESIDUE GOL C 900
23CC5SOFTWARESER B:113 , HIS B:180 , PHE C:130 , GLN C:137 , ASP C:139 , HOH C:296BINDING SITE FOR RESIDUE GOL B 900
24CC6SOFTWARESER A:113 , ASN A:124 , HIS A:180 , HOH A:309 , PHE D:130 , GLN D:137 , ASP D:139 , HOH D:413BINDING SITE FOR RESIDUE GOL A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D4K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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 3D4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D4K)

(-) Exons   (0, 0)

(no "Exon" information available for 3D4K)

(-) 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:237
 aligned with CONA_CANEN | P02866 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:238
                                                                                                                      1                                                                                                                                                   
                                     -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           CONA_CANEN     - ------------------------------------------------------------------------------------------MAISKKSSLFLPIFTFITMFLMVVNKVSSSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d3d4ka_ A: Concanavalin A                                                                                                                                                                                                                      SCOP domains
               CATH domains 3d4kA00 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......eeeeee.hhhhh...eeeeeeeee........eeee-eeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4k A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILS-WSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       109       119       129       139       149       159       169       179       189       199       209       219       229        
                                                                                                                                     108 |                                                                                                                                
                                                                                                                                       109                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with CONA_CANEN | P02866 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:238
                                                                                                                      1                                                                                                                                                   
                                     -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           CONA_CANEN     - ------------------------------------------------------------------------------------------MAISKKSSLFLPIFTFITMFLMVVNKVSSSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d3d4kb_ B: Concanavalin A                                                                                                                                                                                                                      SCOP domains
               CATH domains 3d4kB00 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......eeeeee.hhhhh...eeeeeeeee........eeee-eeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4k B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILS-WSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       109       119       129       139       149       159       169       179       189       199       209       219       229        
                                                                                                                                     108 |                                                                                                                                
                                                                                                                                       109                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with CONA_CANEN | P02866 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:238
                                                                                                                      1                                                                                                                                                   
                                     -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           CONA_CANEN     - ------------------------------------------------------------------------------------------MAISKKSSLFLPIFTFITMFLMVVNKVSSSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d3d4kc_ C: Concanavalin A                                                                                                                                                                                                                      SCOP domains
               CATH domains 3d4kC00 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......eeeeee.hhhhh...eeeeeeeee........eeee-eeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4k C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILS-WSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       109       119       129       139       149       159       169       179       189       199       209       219       229        
                                                                                                                                     108 |                                                                                                                                
                                                                                                                                       109                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:237
 aligned with CONA_CANEN | P02866 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:238
                                                                                                                      1                                                                                                                                                   
                                     -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           CONA_CANEN     - ------------------------------------------------------------------------------------------MAISKKSSLFLPIFTFITMFLMVVNKVSSSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d3d4kd_ D: Concanavalin A                                                                                                                                                                                                                      SCOP domains
               CATH domains 3d4kD00 D: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......eeeeee.hhhhh...eeeeeeeee........eeee-eeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeeee.........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4k D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILS-WSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       109       119       129       139       149       159       169       179       189       199       209       219       229        
                                                                                                                                     108 |                                                                                                                                
                                                                                                                                       109
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4K)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CONA_CANEN | P02866)
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).

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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 ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        CONA_CANEN | P02866: 1apn 1bxh 1c57 1ces 1cjp 1cn1 1con 1cvn 1dq0 1dq1 1dq2 1dq4 1dq5 1dq6 1enq 1enr 1ens 1gic 1gkb 1hqw 1i3h 1jbc 1jn2 1joj 1jui 1jw6 1jyc 1jyi 1nls 1nxd 1ona 1qgl 1qny 1scr 1scs 1tei 1val 1vam 1xqn 2cna 2ctv 2enr 2uu8 2yz4 3cna 3enr 3nwk 4p9w 4p9x 4p9y 4pf5 5cna

(-) Related Entries Specified in the PDB File

1cvn THE SAME LECTIN, CONCANAVALIN A, COMPLEXED TO THE NATIVE TRIMANNOSIDE
1gkb LIGAND-FREE STRUCTURE OF CONCANAVALIN A