1Y2T - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMMON EDIBLE MUSHROOM (AGARICUS BISPORUS) LECTIN

Authors :   M. E. Carrizo, S. Capaldi, M. Perduca, F. J. Irazoqui, G. A. Nores, H. L. M

Date :   23 Nov 04 (Deposition) - 21 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Abl, Agaricus Bisporus, Lectin, Mushroom, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Carrizo, S. Capaldi, M. Perduca, F. J. Irazoqui, G. A. Nores, H. L. Monaco
The Antineoplastic Lectin Of The Common Edible Mushroom (Agaricus Bisporus) Has Two Binding Sites, Each Specific Fo A Different Configuration At A Single Epimeric Hydroxyl
J. Biol. Chem. V. 280 10614 2005
PubMed-ID: 15596442 | Reference-DOI: 10.1074/JBC.M411989200
(for further references see the PDB file header)

Molecule 1 - LECTIN
	Chains	:	A, B
	Organism Scientific	:	AGARICUS BISPORUS
	Organism Taxid	:	5341

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Y2T)

(no "Site" information available for 1Y2T)

(no "SS Bond" information available for 1Y2T)

(no "Cis Peptide Bond" information available for 1Y2T)

(no "SAP(SNP)/Variant" information available for 1Y2T)

(no "PROSITE Motif" information available for 1Y2T)

(no "Exon" information available for 1Y2T)

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:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2ta_ A: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2tA00 A:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeeeee.hhhhh.eeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2t A   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2tb_ B: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2tB00 B:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
           Pfam domains (1) FB_lectin-1y2tB01 B:2-141                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) FB_lectin-1y2tB02 B:2-141                                                                                                                   -- Pfam domains (2)
         Sec.struct. author .eeeeeeeee.......eeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2t B   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cytolysin/lectin (26)

Superfamily: Cytolysin/lectin (26)

Family: Fungal fruit body lectin (17)

Protein domain: TF antigen-binding lectin (5)

Common mushroom (Agaricus bisporus) [TaxId: 5341] (5)

1a	d1y2ta_	A:
1b	d1y2tb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Mutm (Fpg) Protein; Chain: A, domain 2 (18)

Homologous Superfamily: [code=2.60.270.20, no name defined] (18)

Agaricus bisporus. Organism_taxid: 5341 (5)

1a	1y2tA00	A:2-143
1b	1y2tB00	B:2-143

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: FB_lectin] (4)

Family: FB_lectin (4)

Agaricus bisporus (Common mushroom) (2)

1a	FB_lectin-1y2tB01	B:2-141
1b	FB_lectin-1y2tB02	B:2-141

Asymmetric Unit(hide GO term definitions)

Chain A,B (ABL_AGABI | Q00022)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1y2t)

	Sites
(no "Sites" information available for 1y2t)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y2t)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1y2t
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ABL_AGABI \| Q00022
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ABL_AGABI \| Q00022
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ABL_AGABI \| Q00022	:	1y2u 1y2v 1y2w 1y2x

1y2u	THE SAME PROTEIN IN COMPLEX WITH LACTO-N-BIOSE
1y2v	THE SAME PROTEIN IN COMPLEX WITH T-ANTIGEN
1y2w	THE SAME PROTEIN IN COMPLEX WITH T-ANTIGEN AND N- ACETYLGLUCOSAMINE, ORTHORHOMBIC FORM
1y2x	THE SAME PROTEIN IN COMPLEX WITH T-ANTIGEN AND N- ACETYLGLUCOSAMINE, TETRAGONAL FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File