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(-) Description

Title :  CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN I
 
Authors :  K. Harata, W. D. Schubert, M. Muraki
Date :  15 Jul 01  (Deposition) - 07 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Two Homologous Hevein-Like Domains, Zinc Complex, Homo- Dimer, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Harata, W. D. Schubert, M. Muraki
Structure Of Urtica Dioica Agglutinin Isolectin I: Dimer Formation Mediated By Two Zinc Ions Bound At The Sugar-Binding Site.
Acta Crystallogr. , Sect. D V. 57 1513 2001
PubMed-ID: 11679714  |  Reference-DOI: 10.1107/S090744490101232X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGGLUTININ ISOLECTIN I
    ChainsA, B
    FragmentRESIDUES 1-89
    MutationYES
    Organism CommonGREAT NETTLE
    Organism ScientificURTICA DIOICA
    Organism Taxid3501

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:45 , HIS A:47 , HIS B:67 , HOH B:118BINDING SITE FOR RESIDUE ZN A 90
2AC2SOFTWAREASP A:75 , HIS B:47BINDING SITE FOR RESIDUE ZN B 91

(-) SS Bonds  (16, 16)

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
9B:3 -B:18
10B:12 -B:24
11B:17 -B:31
12B:35 -B:39
13B:49 -B:64
14B:58 -B:70
15B:63 -B:77
16B:82 -B:86

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHIT_BIND_I_2PS50941 Chitin-binding type-1 domain profile.AGI_URTDI23-64
69-111
 
  2-
A:46-88
B:46-88
2CHIT_BIND_I_1PS00026 Chitin recognition or binding domain signature.AGI_URTDI35-54
 
81-100
 
  4A:12-31
B:12-31
A:58-77
B:58-77

(-) Exons   (0, 0)

(no "Exon" information available for 1IQB)

(-) 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:89
 aligned with AGI_URTDI | P11218 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:89
                                    33        43        53        63        73        83        93       103         
            AGI_URTDI    24 QRCGSQGGGGTCPALWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGSKCQYRCSSS 112
               SCOP domains d1iqba1 A:1-45 Isolectin VI                  d1iqba2 A:46-89 Isolectin VI                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...hhhhheee....ee.hhhhhh..eee.hhhhh......hhhhh.......eeee....eeehhhhhh...eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: - UniProt: 23-64     ----CHIT_BIND_I_2  PDB: A:46-88 UniProt: 69-111- PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       --------------------------CHIT_BIND_I_1       ------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1iqb A   1 xRCGSQGGGGTCPALWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGSKCQYRCSSS  89
                            |       10        20        30        40        50        60        70        80         
                            |                                                                                        
                            1-PCA                                                                                    

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with AGI_URTDI | P11218 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:89
                                    33        43        53        63        73        83        93       103         
            AGI_URTDI    24 QRCGSQGGGGTCPALWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGSKCQYRCSSS 112
               SCOP domains d1iqbb1 B:1-45 Isolectin VI                  d1iqbb2 B:46-89 Isolectin VI                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...hhhhheee....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: B:46-88 UniProt: 69-111- PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       --------------------------CHIT_BIND_I_1       ------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1iqb B   1 xRCGSQGGGGTCPALWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGSKCQYRCSSS  89
                            |       10        20        30        40        50        60        70        80         
                            1-PCA                                                                                    

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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

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UniProtKB/Swiss-Prot
        AGI_URTDI | P112181en2 1enm

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