1AX0 - JenaLib

Title :   ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH N-ACTYLGALACTOSAMINE

Authors :   B. Shaanan, S. Elgavish

Date :   24 Oct 97 (Deposition) - 06 May 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Lectin, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Elgavish, B. Shaanan
Structures Of The Erythrina Corallodendron Lectin And Of It Complexes With Mono- And Disaccharides.
J. Mol. Biol. V. 277 917 1998
PubMed-ID: 9545381 | Reference-DOI: 10.1006/JMBI.1998.1664

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 10)

Asymmetric Unit (8, 10)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	1	Ligand/Ion	CALCIUM ION
4	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
5	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
6	MN	1	Ligand/Ion	MANGANESE (II) ION
7	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (6, 16)

No.	Name	Count	Type	Full Name
1	A2G	2	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
5	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
6	MN	-1	Ligand/Ion	MANGANESE (II) ION
7	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:6 , ASP A:16 , ASN A:17 , TYR A:53 , FUC A:302 , NAG A:303 , HOH A:561 , HOH A:658	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	LYS A:55 , NAG A:301 , NAG A:303	BINDING SITE FOR RESIDUE FUC A 302
03	AC3	SOFTWARE	ASP A:16 , NAG A:301 , FUC A:302 , BMA A:304 , XYP A:305 , MAN A:307 , HOH A:561	BINDING SITE FOR RESIDUE NAG A 303
04	AC4	SOFTWARE	ASP A:16 , LEU A:18 , THR A:19 , NAG A:303 , XYP A:305 , MAN A:306 , MAN A:307	BINDING SITE FOR RESIDUE BMA A 304
05	AC5	SOFTWARE	ASP A:16 , ALA A:54 , NAG A:303 , BMA A:304 , MAN A:306 , HOH A:658	BINDING SITE FOR RESIDUE XYP A 305
06	AC6	SOFTWARE	ALA A:54 , LYS A:99 , BMA A:304 , XYP A:305 , HOH A:520 , HOH A:662	BINDING SITE FOR RESIDUE MAN A 306
07	AC7	SOFTWARE	GLY A:14 , ASN A:15 , LEU A:18 , THR A:19 , LEU A:20 , NAG A:303 , BMA A:304 , HOH A:528 , HOH A:626	BINDING SITE FOR RESIDUE MAN A 307
08	AC8	SOFTWARE	ASP A:89 , TYR A:106 , GLY A:107 , PHE A:131 , ASN A:133 , GLY A:217 , ALA A:218 , GLN A:219 , HOH A:527 , HOH A:579 , HOH A:613 , HOH A:642	BINDING SITE FOR RESIDUE A2G A 401
09	AC9	SOFTWARE	GLU A:127 , ASP A:129 , ASP A:136 , HIS A:142 , HOH A:500 , HOH A:501	BINDING SITE FOR RESIDUE MN A 289
10	BC1	SOFTWARE	ASP A:129 , PHE A:131 , ASN A:133 , ASP A:136 , HOH A:502 , HOH A:503	BINDING SITE FOR RESIDUE CA A 290

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric 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	P	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)

Biological Unit 1 (3, 6)

								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	P	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)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:239
 aligned with LEC_ERYCO | P16404 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:239
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256         
            LEC_ERYCO    27 VETISFSFSEFEPGNDNLTLQGAALITQSGVLQLTKINQNGMPAWDSTGRTLYAKPVHIWDMTTGTVASFETRFSFSIEQPYTRPLPADGLVFFMGPTKSKPAQGYGYLGIFNNSKQDNSYQTLGVEFDTFSNPWDPPQVPHIGIDVNSIRSIKTQPFQLDNGQVANVVIKYDASSKILHAVLVYPSSGAIYTIAEIVDVKQVLPEWVDVGLSGATGAQRDAAETHDVYSWSFQASLPE 265
               SCOP domains d1ax0a_ A: Legume lectin                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ax0A00 A:1-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee..........................eeeee................eeeeeeee............eeeeee..........hhh..........hhh..eeeeee............eeeeee......eeee.......eeeeeeeee....eeeeeeee....eee.......hhh..................................... Sec.struct. author
                 SAPs(SNPs) ---------------------A---------------------------------------------------------------------------------------------------------------Q----------------------------------------------------------------V---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ax0 A   1 VETISFSFSEFEPGNDNLTLQGAALITQSGVLQLTKINQNGMPAWDSTGRTLYAKPVHIWDMTTGTVASFETRFSFSIEQPYTRPLPADGLVFFMGPTKSKPAQGYGYLGIFNNSKQDNSYQTLGVEFDTFSNPWDPPQVPHIGIDVNSIRSIKTQPFQLDNGQVANVVIKYDASSKILHAVLVYPSSGAIYTIAEIVDVKQVLPEWVDVGLSGATGAQRDAAETHDVYSWSFQASLPE 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

Asymmetric 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.

Visualization

Interactive Views

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
		A2G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		XYP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ 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 ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1ax0
		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

Description