1LOF - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF A BIANTENNARY OCTASACCHARIDE-LECTIN COMPLEX AT 2.3 ANGSTROMS RESOLUTION

Authors :   Y. Bourne, C. Cambillau

Date :   27 Jan 93 (Deposition) - 30 Apr 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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 Biantennary Octasaccharide-Lectin Complex Refined At 2. 3-A Resolution.
J. Biol. Chem. V. 267 197 1992
PubMed-ID: 1730588

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

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

Molecule 3 - LEGUME ISOLECTIN I (ALPHA CHAIN)
	Chains	:	C
	Organ	:	SEED
	Organism Common	:	YELLOW-FLOWERED PEA
	Organism Scientific	:	LATHYRUS OCHRUS
	Organism Taxid	:	3858

Molecule 4 - LEGUME ISOLECTIN I (BETA CHAIN)
	Chains	:	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 (6, 15)

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

Biological Unit 1 (4, 11)

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

Biological Unit 2 (2, 3)

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

Biological Unit 3 (4, 8)

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

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:80 , ASP A:81 , GLY A:98 , GLY A:99 , PHE A:123 , ASN A:125 , BMA A:502 , NAG A:505 , HOH A:824 , GLY B:29 , ALA B:30 , GLU B:31	BINDING SITE FOR RESIDUE MAN A 501
02	AC2	SOFTWARE	PHE A:123 , MAN A:501 , MAN A:503 , NAG A:504 , NAG A:505 , NAG A:508 , HOH A:830 , HOH A:835	BINDING SITE FOR RESIDUE BMA A 502
03	AC3	SOFTWARE	BMA A:502 , NAG A:504 , NAG A:508	BINDING SITE FOR RESIDUE MAN A 503
04	AC4	SOFTWARE	PHE A:123 , TYR A:124 , BMA A:502 , MAN A:503 , GAL A:506 , HOH A:844 , HOH A:854 , GLU B:31	BINDING SITE FOR RESIDUE NAG A 504
05	AC5	SOFTWARE	ASN A:39 , THR A:96 , GLY A:97 , MAN A:501 , BMA A:502 , GAL A:507 , HOH A:824 , HOH A:856 , ALA B:30	BINDING SITE FOR RESIDUE NAG A 505
06	AC6	SOFTWARE	NAG A:505 , HOH A:851	BINDING SITE FOR RESIDUE GAL A 507
07	AC7	SOFTWARE	BMA A:502 , MAN A:503	BINDING SITE FOR RESIDUE NAG A 508
08	AC8	SOFTWARE	TYR A:77 , NAG A:504 , HOH A:809 , HOH A:843 , HOH A:844 , HOH A:847	BINDING SITE FOR RESIDUE GAL A 506
09	AC9	SOFTWARE	ALA C:80 , ASP C:81 , GLY C:98 , GLY C:99 , PHE C:123 , ASN C:125 , MAN C:512 , NAG C:515 , GLY D:29 , ALA D:30 , GLU D:31	BINDING SITE FOR RESIDUE MAN C 511
10	BC1	SOFTWARE	PHE C:123 , MAN C:511 , NAG C:515 , HOH C:791 , ALA D:30	BINDING SITE FOR RESIDUE MAN C 512
11	BC2	SOFTWARE	ASN C:39 , GLY C:97 , GLY C:98 , MAN C:511 , MAN C:512 , HOH C:818 , HOH C:819 , HOH C:821 , GLY D:29 , ALA D:30	BINDING SITE FOR RESIDUE NAG C 515
12	BC3	SOFTWARE	ASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:744 , HOH A:745	BINDING SITE FOR RESIDUE CA A 227
13	BC4	SOFTWARE	GLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:746 , HOH A:747	BINDING SITE FOR RESIDUE MN A 228
14	BC5	SOFTWARE	ASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:681 , HOH C:682	BINDING SITE FOR RESIDUE CA C 457
15	BC6	SOFTWARE	GLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:641 , HOH C:683 , HOH C:684	BINDING SITE FOR RESIDUE MN C 458

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

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 1LOF)

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: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 d1lof.1 A:,B: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1lofA00 A:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeee........hhhhh..............eeeeee..............eeeeee......eeee.............................. Sec.struct. author
                 SAPs(SNPs) ---------------P-------------------------------------------------A-----------------------------------------------------------------------------------------------------G------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lof A   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWALQNGKEANVVIAFNAATNVLTVSLTYPN 181
                                    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:47
 aligned with LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:47
                                    10        20        30        40       
           LEC1_LATOC     1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELA  47
               SCOP domains d1lof.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
                 1lof B   1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELA  47
                                    10        20        30        40

Chain C 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 d1lof.2 C:,D: Legume lectin                                                                                                                                                          SCOP domains
               CATH domains 1lofC00 C:1-180  [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
                 1lof C   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWKLQNGKEANVVIAFNAATNVLTVSLTYP 180
                                    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:52
 aligned with LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:52
                                    10        20        30        40        50  
           LEC1_LATOC     1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELAGTSSS  52
               SCOP domains d1lof.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
                 1lof D   1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELAGTSSN  52
                                    10        20        30        40        50

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: 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	d1lof.1	A:,B:
1b	d1lof.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	1lofA00	A:1-181
1b	1lofC00	C:1-180

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:80 - Asp A:81	[ RasMol ]
		Ala C:80 - Asp C:81	[ RasMol ]

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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LEC1_LATOC \| P12306	:	1loa 1lob 1loc 1lod 1loe 1log
	LECB_LATOC \| P04122	:	1lgb 1lgc 1loa 1lob 1loc 1lod 1loe 1log

(no "Related Entries Specified in the PDB File" available for 1LOF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (3, 5)

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