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Biological Unit 3 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF A (ALPHA-MAN(1-3)BETA-MAN(1-4)GLCNAC)-LECTIN COMPLEX AT 2.1 ANGSTROMS RESOLUTION

Authors :   Y. Bourne, C. Cambillau

Date :   27 Jan 94 (Deposition) - 30 Apr 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B  (1x)

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

Reference :   Y. Bourne, P. Rouge, C. Cambillau
X-Ray Structure Of A (Alpha-Man(1-3)Beta-Man(1-4)Glcnac)-Lectin Complex At 2. 1-A Resolution. The Role Of Water In Sugar-Lectin Interaction.
J. Biol. Chem. V. 265 18161 1990
PubMed-ID: 2211692
(for further references see the PDB file header)

Molecule 1 - LEGUME ISOLECTIN I (ALPHA CHAIN)
	Chains	:	A, C
	Organ	:	SEED
	Organism Common	:	YELLOW-FLOWERED PEA
	Organism Scientific	:	LATHYRUS OCHRUS
	Organism Taxid	:	3858

Molecule 2 - LEGUME ISOLECTIN I (BETA CHAIN)
	Chains	:	B, D
	Organ	:	SEED
	Organism Common	:	YELLOW-FLOWERED PEA
	Organism Scientific	:	LATHYRUS OCHRUS
	Organism Taxid	:	3858

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CA	2	Ligand/Ion	CALCIUM ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	2	Ligand/Ion	MANGANESE (II) ION
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA C:80 , ASP C:81 , GLY C:98 , GLY C:99 , PHE C:123 , ASN C:125 , BMA C:582 , HOH C:877 , HOH C:909 , HOH C:915 , GLY D:29 , ALA D:30 , GLU D:31	BINDING SITE FOR RESIDUE MAN C 581
02	AC2	SOFTWARE	ASP A:134 , PHE C:123 , MAN C:581 , NAG C:583 , HOH C:908	BINDING SITE FOR RESIDUE BMA C 582
03	AC3	SOFTWARE	BMA C:582 , HOH C:918 , HOH C:919 , HOH C:921 , HOH C:923 , HOH C:924 , GLU D:31	BINDING SITE FOR RESIDUE NAG C 583
04	AC4	SOFTWARE	ALA A:80 , ASP A:81 , GLY A:98 , GLY A:99 , PHE A:123 , ASN A:125 , BMA A:592 , GLY B:29 , ALA B:30 , GLU B:31 , HOH C:714	BINDING SITE FOR RESIDUE MAN A 591
05	AC5	SOFTWARE	MAN A:591 , NAG A:593 , HOH A:930 , ASP C:23 , LYS C:35 , VAL C:37	BINDING SITE FOR RESIDUE BMA A 592
06	AC6	SOFTWARE	BMA A:592 , HOH A:930 , HOH A:933 , ALA B:30 , GLU B:31	BINDING SITE FOR RESIDUE NAG A 593
07	AC7	SOFTWARE	ASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:745 , HOH A:746	BINDING SITE FOR RESIDUE CA A 561
08	AC8	SOFTWARE	GLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:747 , HOH A:748	BINDING SITE FOR RESIDUE MN A 562
09	AC9	SOFTWARE	ASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:762 , HOH C:763	BINDING SITE FOR RESIDUE CA C 571
10	BC1	SOFTWARE	GLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:764 , HOH C:765	BINDING SITE FOR RESIDUE MN C 572

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

Asymmetric Unit

No.	Residues
1	Ala A:80	-	Asp A:81
2	Ala C:80	-	Asp C:81

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECB_LATOC_001 *	Q	16	P	LECB_LATOC	---	---	A/C	Q	16	P
2	UniProt	VAR_LECB_LATOC_002 *	S	66	A	LECB_LATOC	---	---	A/C	S	66	A
3	UniProt	VAR_LECB_LATOC_003 *	A	168	G	LECB_LATOC	---	---	A/C	A	168	G
	* 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_LECB_LATOC_001 *	Q	16	P	LECB_LATOC	---	---	A/C	Q	16	P
2	UniProt	VAR_LECB_LATOC_002 *	S	66	A	LECB_LATOC	---	---	A/C	S	66	A
3	UniProt	VAR_LECB_LATOC_003 *	A	168	G	LECB_LATOC	---	---	A/C	A	168	G
	* ID not provided by source

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECB_LATOC_001 *	Q	16	P	LECB_LATOC	---	---	C	Q	16	P
2	UniProt	VAR_LECB_LATOC_002 *	S	66	A	LECB_LATOC	---	---	C	S	66	A
3	UniProt	VAR_LECB_LATOC_003 *	A	168	G	LECB_LATOC	---	---	C	A	168	G
	* ID not provided by source

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

Biological Unit 3 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECB_LATOC_001 *	Q	16	P	LECB_LATOC	---	---	A	Q	16	P
2	UniProt	VAR_LECB_LATOC_002 *	S	66	A	LECB_LATOC	---	---	A	S	66	A
3	UniProt	VAR_LECB_LATOC_003 *	A	168	G	LECB_LATOC	---	---	A	A	168	G
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC1_LATOC	16-25	2	B:16-25 D:16-25
2	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECB_LATOC	116-122	2	A:116-122 C:116-122

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC1_LATOC	16-25	2	B:16-25 D:16-25
2	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECB_LATOC	116-122	2	A:116-122 C:116-122

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC1_LATOC	16-25	1	- D:16-25
2	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECB_LATOC	116-122	1	- C:116-122

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC1_LATOC	16-25	1	B:16-25 -
2	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECB_LATOC	116-122	1	A:116-122 -

(no "Exon" information available for 1LOG)

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:180
 aligned with LECB_LATOC | P04122 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           LECB_LATOC     1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWKLQNGKEANVVIAFNAATNVLTVSLTYP 180
               SCOP domains d1log.1 A:,B: Legume lectin                                                                                                                                                          SCOP domains
               CATH domains 1logA00 A:1-180  [code=2.60.120.200, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh........hhhhh.eeeeee..............eeeeee......eeee............................. Sec.struct. author
                 SAPs(SNPs) ---------------P-------------------------------------------------A-----------------------------------------------------------------------------------------------------G------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1log A   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWALQNGKEANVVIAFNAATNVLTVSLTYP 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:46
                                    11        21        31        41      
           LEC1_LATOC     2 TSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELA  47
               SCOP domains d1log.1 A:,B: Legume lectin                    SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE --------------LECTIN_LEG---------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1log B   2 TSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELA  47
                                    11        21        31        41

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with LECB_LATOC | P04122 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           LECB_LATOC     1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWKLQNGKEANVVIAFNAATNVLTVSLTYPN 181
               SCOP domains d1log.2 C:,D: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1logC00 C:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh..............eeeeee..............eeeeee......eeee.............................. Sec.struct. author
                 SAPs(SNPs) ---------------P-------------------------------------------------A-----------------------------------------------------------------------------------------------------G------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1log C   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWALQNGKEANVVIAFNAATNVLTVSLTYPN 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:51
 aligned with LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:51
                                    10        20        30        40        50 
           LEC1_LATOC     1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELAGTSS  51
               SCOP domains d1log.2 C:,D: Legume lectin                         SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh...eeeeeeeee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG-------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 1log D   1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELAGTSS  51
                                    10        20        30        40        50

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: Legume lectins (238)

Protein domain: Legume lectin (110)

Lathyrus ochrus, isolectin I [TaxId: 3858] (7)

1a	d1log.1	A:,B:
1b	d1log.2	C:,D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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)

Yellow-flowered pea (Lathyrus ochrus) (8)

1a	1logC00	C:1-181
1b	1logA00	A:1-180

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (LECB_LATOC | P04122)


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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Chain B,D (LEC1_LATOC | P12306)

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:0005537		mannose binding		Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.

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		Ala A:80 - Asp A:81	[ RasMol ]
		Ala C:80 - Asp C:81	[ RasMol ]

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