3N36 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ERYTHRINA CORALLODENDRON LECTIN MUTANT (Y106G) IN COMPLEX WITH GALACTOSE

Authors :   S. Thamotharan, T. Karthikeyan, K. A. Kulkarni, K. N. Shetty, A. Suroli M. Vijayan, K. Suguna

Date :   19 May 10 (Deposition) - 30 Mar 11 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Legume Lectin, Glycosylation, Erythrina Lectin, Sugar, Recombinant Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Thamotharan, T. Karthikeyan, K. A. Kulkarni, K. N. Shetty, A. Surolia, M. Vijayan, K. Suguna
Modification Of The Sugar Specificity Of A Plant Lectin: Structural Studies On A Point Mutant Of Erythrina Corallodendron Lectin.
Acta Crystallogr. , Sect. D V. 67 218 2011
PubMed-ID: 21358053 | Reference-DOI: 10.1107/S0907444911004525

Molecule 1 - LECTIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	MECORL
	Mutation	:	YES
	Organism Common	:	CORAL TREE
	Organism Scientific	:	ERYTHRINA CORALLODENDRON
	Organism Taxid	:	3843

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
3	MN	1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:127 , ASP A:129 , ASP A:136 , HIS A:142 , HOH A:243 , HOH A:244	BINDING SITE FOR RESIDUE MN A 289
2	AC2	SOFTWARE	ASP A:129 , PHE A:131 , ASN A:133 , ASP A:136 , HOH A:245 , HOH A:246	BINDING SITE FOR RESIDUE CA A 290
3	AC3	SOFTWARE	ASP A:89 , GLY A:107 , ASN A:133 , GLY A:217 , ALA A:218 , GLN A:219 , ALA A:222 , HOH A:247 , HOH A:376 , HOH A:390	BINDING SITE FOR RESIDUE GLA A 401

(no "SS Bond" information available for 3N36)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:84	-	Pro A:85
2	Ala A:88	-	Asp A:89
3	Val A:140	-	Pro A:141

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LEC_ERYCO_001 *	G	48	A	LEC_ERYCO	---	---	A	G	22	A
2	UniProt	VAR_LEC_ERYCO_002 *	P	160	Q	LEC_ERYCO	---	---	A	Q	134	Q
3	UniProt	VAR_LEC_ERYCO_003 *	D	225	V	LEC_ERYCO	---	---	A	D	199	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_ERYCO	150-156	1	A:124-130
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC_ERYCO	230-239	1	A:204-213

(no "Exon" information available for 3N36)

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 LEC_ERYCO | P16404 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:242
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  
            LEC_ERYCO    27 VETISFSFSEFEPGNDNLTLQGAALITQSGVLQLTKINQNGMPAWDSTGRTLYAKPVHIWDMTTGTVASFETRFSFSIEQPYTRPLPADGLVFFMGPTKSKPAQGYGYLGIFNNSKQDNSYQTLGVEFDTFSNPWDPPQVPHIGIDVNSIRSIKTQPFQLDNGQVANVVIKYDASSKILHAVLVYPSSGAIYTIAEIVDVKQVLPEWVDVGLSGATGAQRDAAETHDVYSWSFQASLPETND 268
               SCOP domains d3n36a_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Lectin_legB-3n36A01 A:2-234                                                                                                                                                                                                              -------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.ee....ee.eeeeeeeee...........eeeeeeeee.......hhhhh........hhhhh.eeeeee............eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------A---------------------------------------------------------------------------------------------------------------Q----------------------------------------------------------------V------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n36 A   1 VETISFSFSEFEPGNDNLTLQGASLITQSGVLQLTKINQNGMPAWDSTGRTLYAKPVHIWDMTTGTVASFETRFSFSIEQPYTRPLPADGLVFFMGPTKSKPAQGGGYLGIFNNSKQDNSYQTLGVEFDTFSNQWDPPQVPHIGIDVNSIRSIKTQPFQLDNGQVANVVIKYDASSKILHAVLVYPSSGAIYTIAEIVDVKQVLPEWVDVGLSGATGAQRDAAETHDVYSWSFQASLPETND 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Legume lectins (238)

Protein domain: automated matches (63)

Coral tree (Erythrina corallodendron) [TaxId: 3843] (3)

d3n36a_

(no "CATH Domain" information available for 3N36)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Lectin_legB (93)

Erythrina corallodendrum (Coral tree) (5)

Lectin_legB-3n36A01

A:2-234

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LEC_ERYCO | P16404)

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/Biological 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:88 - Asp A:89	[ RasMol ]
		Arg A:84 - Pro A:85	[ RasMol ]
		Val A:140 - Pro A:141	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	3n36
		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
	LEC_ERYCO \| P16404
		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
	LEC_ERYCO \| P16404
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LEC_ERYCO \| P16404	:	1ax0 1ax1 1ax2 1axy 1axz 1fyu 1lte 1sfy 3n35 3n3h

1ax0	ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH N- ACTYLGALACTOSAMINE
1ax1	ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH LACTOSE
1fyu	CRYSTAL STRUCTURE OF ERYTHRINA CORALLODENDRON LECTIN IN HEXAGONAL CRYSTAL FORM
1sfy	CRYSTAL STRUCTURE OF RECOMBINANT ERYTHRINA CORALLODENDRON LECTIN
3n35
3n3h

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

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