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(-) Description

Title :  CRYSTAL STRUCTURE OF CONCANAVALIN A COMPLEXED WITH A SYNTHETIC DERIVATIVE OF HIGH-MANNOSE CHAIN
 
Authors :  P. Lafite, R. Daniellou
Date :  28 Apr 14  (Deposition) - 17 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Sugar Binding Protein, Lectin, High Mannose (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Francois-Heude, A. Mendez-Ardoy, V. Cendret, P. Lafite, R. Daniellou, C. Ortiz Mellet, J. M. Garcia Fernandez, V. Moreau, F. Djedaini-Pilard
Synthesis Of High-Mannose Oligosaccharide Analogues Through Click Chemistry: True Functional Mimics Of Their Natural Counterparts Against Lectins?
Chemistry V. 21 1978 2015
PubMed-ID: 25483029  |  Reference-DOI: 10.1002/CHEM.201405481

(-) Compounds

Molecule 1 - CONCANAVALIN-A
    Chains: A, B
    Fragment: RESIDUES 164-281, 30-148
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Synonym: CON A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2M3N2Ligand/Ion4-(HYDROXYMETHYL)-1-(ALPHA-D-MANNOPYRANOSYL)-1H-1,2,3-TRIAZOLE
3MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2M3N4Ligand/Ion4-(HYDROXYMETHYL)-1-(ALPHA-D-MANNOPYRANOSYL)-1H-1,2,3-TRIAZOLE
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:435 , HOH A:436binding site for residue MN A 301
2AC2SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:433 , HOH A:434binding site for residue MN A 302
3AC3SOFTWARETYR 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:475 , HOH A:524 , HOH A:525binding site for residue M3N A 303
4AC4SOFTWARESER A:113 , ASN A:124 , VAL A:179 , HIS A:180 , HOH A:455binding site for residue EDO A 304
5AC5SOFTWARETYR 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:445 , HOH B:498binding site for residue M3N B 301
6AC6SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:423 , HOH B:424binding site for residue MN B 302
7AC7SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:421 , HOH B:422binding site for residue MN B 303
8AC8SOFTWARESER B:113 , VAL B:179 , HIS B:180 , HOH B:457binding site for residue EDO B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PF5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:207 -Asp A:208
2Ala B:207 -Asp B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PF5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PF5)

(-) 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
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee......eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.........eeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pf5 A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pf5 B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 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)
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  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  (0, 0)

(no "SCOP Domain" information available for 4PF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PF5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:207 - Asp A: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 3d4k 3enr 3nwk 4p9w 4p9x 4p9y 5cna

(-) Related Entries Specified in the PDB File

3d4k CONA COMPLEXED WITH A TRIMANNOSIDE ANALOGUE (CRYSTALLIZED UNDER THE SAME CONDITIONS).