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(-) Description

Title :  STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH A TRIMANNOSIDE
 
Authors :  R. G. Benevides, G. Ganne, C. Unverzagt, B. S. Cavada, C. Breton, A. Varr A. Imberty
Date :  28 Jul 11  (Deposition) - 11 Jan 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Binding Protein, Plant Lectin, N-Glycan (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Benevides, G. Ganne, R. D. C. Simoes, V. Schubert, M. Niemietz, C. Unverzagt, V. Chazalet, C. Breton, A. Varrot, B. S. Cavada, A. Imberty
A Lectin From Platypodium Elegans With Unusual Specificity And Affinity For Asymmetric Complex N-Glycans.
J. Biol. Chem. V. 287 26352 2012
PubMed-ID: 22692206  |  Reference-DOI: 10.1074/JBC.M112.375816

(-) Compounds

Molecule 1 - LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET29A
    Expression System Vector Type: PLASMID
    Organism Scientific: PLATYPODIUM ELEGANS
    Organism Taxid: 115002
    Other Details: BRASILIAN FLORA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3MAN3Ligand/IonALPHA-D-MANNOSE
4MN2Ligand/IonMANGANESE (II) ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:137 , ASP A:139 , ASP A:150 , HIS A:155 , HOH A:2114 , HOH A:2115BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREASP A:139 , PHE A:141 , ASN A:147 , ASP A:150 , HOH A:2090 , HOH A:2101BINDING SITE FOR RESIDUE CA A 301
3AC3SOFTWAREARG A:21 , ARG A:53 , HOH A:2015 , HOH A:2173BINDING SITE FOR RESIDUE SO4 A 305
4AC4SOFTWAREPRO A:109 , SER A:110 , ASN A:121BINDING SITE FOR RESIDUE GOL A 306
5AC5SOFTWAREGLN A:144 , ASN A:145 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A 307
6AC6SOFTWAREGLU B:137 , ASP B:139 , ASP B:150 , HIS B:155 , HOH B:2096 , HOH B:2097BINDING SITE FOR RESIDUE MN B 300
7AC7SOFTWAREASP B:139 , PHE B:141 , ASN B:147 , ASP B:150 , HOH B:2068 , HOH B:2082BINDING SITE FOR RESIDUE CA B 301
8AC8SOFTWAREARG B:53 , TRP B:68 , LEU B:90 , GLN B:231 , HOH B:2036BINDING SITE FOR RESIDUE GOL B 306
9AC9SOFTWAREALA A:94 , ASP A:95 , GLY A:115 , PHE A:141 , ASN A:145 , SER A:146 , ASN A:147 , GLY A:229 , GLU A:230 , GLN A:231 , HOH A:2100 , HOH A:2172 , ALA B:94 , ASP B:95 , GLY B:115 , PHE B:141 , ASN B:145 , SER B:146 , ASN B:147 , GLY B:229 , GLU B:230 , GLN B:231 , HOH B:2081BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 302 TO 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:94 -Asp A:95
2Ala B:94 -Asp B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZVX)

(-) 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:242
 aligned with G1EUI6_9FABA | G1EUI6 from UniProtKB/TrEMBL  Length:261

    Alignment length:242
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  
         G1EUI6_9FABA     8 STDSLSFSFINFDRDERNLIFQGDAHTSRNNILQLTRTDSNGAPVRSTVGRILHSAQVRLWEKSTNRVANLQTQFSFFLSSPLSNPADGIAFFIAPPDTTIPSGSAGGLLGLFNPRTALNESANQVLAVEFDTFFAQNSNTWDPNYQHIGIDVNSIRSSKVVRWERREGKTLNVLVTYNPSTRTIDVVATYPDGQRYQLSHVVDLTTILPEWVRVGFSAASGEQFQTHNLESWSFTSTLLYT 249
               SCOP domains d3zvxa_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.........eeeee..eee...eee.............eeeeeee.....eee....eeeeeeeeeeeeee........eeeeeee........................hhhhh..eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvx A   8 STDSLSFSFINFDRDERNLIFQGDAHTSRNNILQLTRTDSNGAPVRSTVGRILHSAQVRLWEKSTNRVANLQTQFSFFLSSPLSNPADGIAFFIAPPDTTIPSGSAGGLLGLFNPRTALNESANQVLAVEFDTFFAQNSNTWDPNYQHIGIDVNSIRSSKVVRWERREGKTLNVLVTYNPSTRTIDVVATYPDGQRYQLSHVVDLTTILPEWVRVGFSAASGEQFQTHNLESWSFTSTLLYT 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with G1EUI6_9FABA | G1EUI6 from UniProtKB/TrEMBL  Length:261

    Alignment length:241
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 
         G1EUI6_9FABA     9 TDSLSFSFINFDRDERNLIFQGDAHTSRNNILQLTRTDSNGAPVRSTVGRILHSAQVRLWEKSTNRVANLQTQFSFFLSSPLSNPADGIAFFIAPPDTTIPSGSAGGLLGLFNPRTALNESANQVLAVEFDTFFAQNSNTWDPNYQHIGIDVNSIRSSKVVRWERREGKTLNVLVTYNPSTRTIDVVATYPDGQRYQLSHVVDLTTILPEWVRVGFSAASGEQFQTHNLESWSFTSTLLYT 249
               SCOP domains d3zvxb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..eee...eee.............eeeeeee.....eee....eeeeeeeeeeeeee........eeeeeee........................hhhhh..eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvx B   9 TDSLSFSFINFDRDERNLIFQGDAHTSRNNILQLTRTDSNGAPVRSTVGRILHSAQVRLWEKSTNRVANLQTQFSFFLSSPLSNPADGIAFFIAPPDTTIPSGSAGGLLGLFNPRTALNESANQVLAVEFDTFFAQNSNTWDPNYQHIGIDVNSIRSSKVVRWERREGKTLNVLVTYNPSTRTIDVVATYPDGQRYQLSHVVDLTTILPEWVRVGFSAASGEQFQTHNLESWSFTSTLLYT 249
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G1EUI6_9FABA | G1EUI6)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  Cis Peptide Bonds
    Ala A:94 - Asp A:95   [ RasMol ]  
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  3zvx
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 Related Entries

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

UniProtKB/TrEMBL
        G1EUI6_9FABA | G1EUI6: 3zyr

(-) Related Entries Specified in the PDB File

3zyr STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH HEPTASACCHARIDE