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(-) Description

Title :  UDA TRISACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II
 
Authors :  F. A. Saul, P. Rovira, G. Boulot, E. J. M. Van Damme, W. J. Peumans, P. Tru Bachi, G. A. Bentley
Date :  21 Mar 00  (Deposition) - 21 Jun 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Lectin, Hevein Domain, Uda, Superantigen, Saccharide Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. A. Saul, P. Rovira, G. Boulot, E. J. M. Van Damme, W. J. Peumans, P. Truffa-Bachi, G. A. Bentley
Crystal Structure Of Urtica Dioica Agglutinin, A Superantigen Presented By Mhc Molecules Of Class I And Clas Ii.
Structure Fold. Des. V. 8 593 2000
PubMed-ID: 10873861  |  Reference-DOI: 10.1016/S0969-2126(00)00142-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI
    ChainsA
    Organism CommonGREAT NETTLE
    Organism ScientificURTICA DIOICA
    Organism Taxid3501
    Other DetailsTHREE ISOFORMS ARE PRESENT IN THE CRYSTAL: ISOLECTIN I, V, AND VI
    Other Details - SourcePURIFIED FROM RHIZOMES
    SynonymUDA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPCA A:1 , TRP A:23 , CYS A:24 , SER A:65 , HIS A:67 , TRP A:69 , ASP A:75 , TYR A:76 , NAG A:91 , HOH A:104 , HOH A:125 , HOH A:127BINDING SITE FOR RESIDUE NAG A 90
2AC2SOFTWARESER A:19 , TRP A:21 , TRP A:23 , TYR A:30 , HIS A:67 , NAG A:90 , NAG A:92 , HOH A:96BINDING SITE FOR RESIDUE NAG A 91
3AC3SOFTWARETRP A:21 , NAG A:91BINDING SITE FOR RESIDUE NAG A 92

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:18
2A:12 -A:24
3A:17 -A:31
4A:35 -A:39
5A:49 -A:64
6A:58 -A:70
7A:63 -A:77
8A:82 -A:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ENM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ENM)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHIT_BIND_I_2PS50941 Chitin-binding type-1 domain profile.AGI_URTDI23-64
69-111
  1-
A:46-86
2CHIT_BIND_I_1PS00026 Chitin recognition or binding domain signature.AGI_URTDI35-54
81-100
  2A:12-31
A:58-77

(-) Exons   (0, 0)

(no "Exon" information available for 1ENM)

(-) 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:91
 aligned with AGI_URTDI | P11218 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:91
                                             39                                                                        
                                           38 |                                                                        
                                     33   37| |                                                               103      
                                   32 | 36 || |                                                            102  |      
                                    |-|  | || 40        50        60        70        80        90       100 |  |  108 
            AGI_URTDI    24 QRCGSQGGG-GTCP-AL-WCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSG--SKCQYRC 109
               SCOP domains d1enma1 A11-45IIsllectin VI                     d1enma2 A:46-86 Isolectin VI                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhh..eee....ee.hhhhhh..eee.hhhhh......hhhhh........eee....ee.hhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: - UniProt: 23-64        ----CHIT_BIND_I_2  PDB: A:46-86 UniProt: 69-111 PROSITE (1)
                PROSITE (2) ------------CHIT_BIND_I_1         --------------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1enm A   1 xRCGSQGGGSGTCPGALRWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGSNKCQYRC  86
                            |       10        17        27        37        47        57        67        77        85 
                            |                                                                                          
                            1-PCA                                                                                      

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  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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ENM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ENM)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGI_URTDI | P11218)
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:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    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).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGI_URTDI | P112181en2 1iqb

(-) Related Entries Specified in the PDB File

1eis UDA UNCOMPLEXED FORM
1en2 UDA TETRASACCHARIDE COMPLEX