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Title :   STRUCTURAL BASIS OF CARBOHYDRATE RECOGNITION BY BOWRINGIA MILBRAEDII SEED AGGLUTININ

Authors :   L. Buts, A. Garcia-Pino, L. Wyns, R. Loris

Date :   09 Jan 06 (Deposition) - 22 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Legume Lectin, Beta Sandwich, Protein-Carbohydrate Complex, Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Buts, A. Garcia-Pino, L. Wyns, R. Loris
Structural Basis Of Carbohydrate Recognition By A Man(Alpha1-2)Man-Specific Lectin From Bowringia Milbraedii.
Glycobiology V. 16 635 2006
PubMed-ID: 16567368 | Reference-DOI: 10.1093/GLYCOB/CWJ109
(for further references see the PDB file header)

Molecule 1 - LECTIN
	Chains	:	A
	Organism Scientific	:	BOWRINGIA MILDBRAEDII
	Organism Taxid	:	28956
	Synonym	:	AGGLUTININ, BMA
	Tissue	:	SEED

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	ASX	2	Mod. Amino Acid
2	CA	1	Ligand/Ion	CALCIUM ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	ASX	-1	Mod. Amino Acid
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAN	8	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:85 , ASP A:86 , GLY A:105 , ARG A:106 , TYR A:131 , ASN A:133 , SER A:189 , SER A:190 , GLY A:217 , GLN A:218 , TYR A:219 , MAN A:242 , HOH A:373	BINDING SITE FOR RESIDUE MAN A 241
2	AC2	SOFTWARE	SER A:62 , TYR A:131 , ASN A:188 , SER A:189 , GLN A:218 , MAN A:241 , HOH A:421	BINDING SITE FOR RESIDUE MAN A 242
3	AC3	SOFTWARE	ASP A:129 , TYR A:131 , ASN A:133 , ASP A:138 , HOH A:425 , HOH A:426	BINDING SITE FOR RESIDUE CA A 301
4	AC4	SOFTWARE	GLU A:127 , ASP A:129 , ASP A:138 , HIS A:143 , HOH A:423 , HOH A:424	BINDING SITE FOR RESIDUE MN A 302

(no "SS Bond" information available for 2FMD)

Asymmetric Unit

No.	Residues
1	Ala A:85	-	Asp A:86

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LEC_LEUMI_001 *	H	143	S	LEC_LEUMI	---	---	A	H	143	S
2	UniProt	VAR_LEC_LEUMI_002 *	K	158	R	LEC_LEUMI	---	---	A	K	158	R
3	UniProt	VAR_LEC_LEUMI_003 *	S	177	R	LEC_LEUMI	---	---	A	S	177	R
4	UniProt	VAR_LEC_LEUMI_004 *	P	187	V	LEC_LEUMI	---	---	A	P	187	V
5	UniProt	VAR_LEC_LEUMI_005 *	V	203	A	LEC_LEUMI	---	---	A	V	203	A
	* ID not provided by source

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

Biological Unit 1 (5, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LEC_LEUMI_001 *	H	143	S	LEC_LEUMI	---	---	A	H	143	S
2	UniProt	VAR_LEC_LEUMI_002 *	K	158	R	LEC_LEUMI	---	---	A	K	158	R
3	UniProt	VAR_LEC_LEUMI_003 *	S	177	R	LEC_LEUMI	---	---	A	S	177	R
4	UniProt	VAR_LEC_LEUMI_004 *	P	187	V	LEC_LEUMI	---	---	A	P	187	V
5	UniProt	VAR_LEC_LEUMI_005 *	V	203	A	LEC_LEUMI	---	---	A	V	203	A
	* ID not provided by source

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_LEUMI	124-130	1	A:124-130

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_LEUMI	124-130	4	A:124-130

(no "Exon" information available for 2FMD)

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:232
 aligned with LEC_LEUMI | P42088 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
            LEC_LEUMI     1 ANSVCFTFTDFESGQQDLIFQGDASVGSNKALQLTKVDSKGNPQGGSVGRALYTAPIRLWQSSSLVASFETTFTFSISQGSSTPAAALTFFIASPDTKIPSGSGGRLLGLFGSSNNAGSDNGVVAVEFDTYPNTDIGDPNYRHIGIDVNSIRSKAASKWDWQNGKTATAHISYNSASKRLSVVSSYPNSSPVVVSFDVELNNVGPPDVRVGFSATTGQYTQTNNILAWSFRSSLMG 236
               SCOP domains d2fmda_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2fmdA00 A:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh.......----...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------S--------------R------------------R---------V---------------A--------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmd A   1 ANSVCFTFTDFESGQQDLIFQGDASVGSNKALQLTKVDSKGNPQGGSVGRALYTAPIRLWQSSSLVASFETTFTFSISQGSSTPADALTFFIASPDTKIPSGSGGRLLGLFGSSN----DNGVVSVEFDTYPNTDIGDPNYRHIGIDVNSIRSKAASKWDWQNGKTATAHISYNSASKRLSVVSSYPNSSPVVVSFDVELNNVxPxWVRVGFSATTGQYTQTNNILAWSFRSSLMG 236
                                    10        20        30        40        50        60        70        80        90       100       110    |  120       130       140       150       160       170       180       190       200   | | 210       220       230      
                                                                                                                                            115  120                                                                                 204-ASX                            
                                                                                                                                                                                                                                       206-ASX

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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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: automated matches (133)

Protein domain: automated matches (133)

Bowringia mildbraedii [TaxId: 28956] (1)

d2fmda_

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Bowringia mildbraedii. Organism_taxid: 28956. (1)

2fmdA00

A:1-236

(no "Pfam Domain" information available for 2FMD)

Asymmetric Unit(hide GO term definitions)

Chain A (LEC_LEUMI | P42088)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:85 - Asp A:86	[ RasMol ]

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