1JPC - JenaLib

Title :   MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE

Authors :   C. S. Wright, G. Hester

Date :   30 Jul 96 (Deposition) - 27 Jan 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (4x)

Keywords :   Lectin, Agglutinin, Mannopentaose, (Mannose-Alpha1, 6-(Mannose-Alpha1, 3-Mannose- Alpha1, 6-(Mannose-Alpha1, 3)-Mannose), Snowdrop (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. S. Wright, G. Hester
The 2. 0 A Structure Of A Cross-Linked Complex Between Snowdrop Lectin And A Branched Mannopentaose: Evidence For Two Unique Binding Modes.
Structure V. 4 1339 1996
PubMed-ID: 8939757 | Reference-DOI: 10.1016/S0969-2126(96)00141-4
(for further references see the PDB file header)

Compounds

Molecule 1 - AGGLUTININ
	Chains	:	A
	Organism Common	:	COMMON SNOWDROP
	Organism Scientific	:	GALANTHUS NIVALIS
	Organism Taxid	:	4670
	Other Details	:	FROM GALANTHUS NIVALIS PLANT FAMILY OF AMARYLLIDACEAE
	Other Details - Source	:	THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY OF AMARYLLIDACEAE. THE PROTEIN IS ISOLATED FROM THE BULBS.
	Synonym	:	SNOWDROP LECTIN

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:83 , HIS A:107 , MAN A:111 , MAN A:112	BINDING SITE FOR RESIDUE MAN A 110
2	AC2	SOFTWARE	ASN A:83 , GLN A:89 , ASP A:91 , ASN A:93 , TYR A:97 , ASP A:100 , ALA A:103 , MAN A:110 , MAN A:112 , HOH A:135	BINDING SITE FOR RESIDUE MAN A 111
3	AC3	SOFTWARE	ASN A:83 , GLN A:89 , ASP A:91 , ASN A:93 , TYR A:97 , ASP A:100 , MAN A:110 , MAN A:111	BINDING SITE FOR RESIDUE MAN A 112
4	AC4	SOFTWARE	GLN A:57 , ASP A:59 , ASN A:61 , TYR A:65 , MAN A:114 , HOH A:158 , HOH A:170	BINDING SITE FOR RESIDUE MAN A 113
5	AC5	SOFTWARE	PRO A:71 , TRP A:73 , ALA A:74 , ASN A:76 , MAN A:113 , HOH A:162	BINDING SITE FOR RESIDUE MAN A 114
6	AC6	SOFTWARE	GLN A:26 , ASP A:28 , ASN A:30 , TYR A:34 , PRO A:39 , MAN A:116 , MAN A:117 , HOH A:172	BINDING SITE FOR RESIDUE MAN A 115
7	AC7	SOFTWARE	GLN A:26 , TYR A:34 , ASP A:37 , LYS A:38 , MAN A:115 , HOH A:125 , HOH A:134	BINDING SITE FOR RESIDUE MAN A 116
8	AC8	SOFTWARE	PRO A:39 , ASN A:44 , MAN A:115	BINDING SITE FOR RESIDUE MAN A 117

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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_GALNI_002 *	S	74	H	LEC_GALNI	---	---	A	S	51	H
2	UniProt	VAR_LEC_GALNI_003 *	F	76	Y	LEC_GALNI	---	---	A	F	53	Y
3	UniProt	VAR_LEC_GALNI_004 *	C	109	S	LEC_GALNI	---	---	A	C	86	S
	* ID not provided by source

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

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LEC_GALNI_002 *	S	74	H	LEC_GALNI	---	---	A	S	51	H
2	UniProt	VAR_LEC_GALNI_003 *	F	76	Y	LEC_GALNI	---	---	A	F	53	Y
3	UniProt	VAR_LEC_GALNI_004 *	C	109	S	LEC_GALNI	---	---	A	C	86	S
	* ID not provided by source

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

Biological Unit 2 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LEC_GALNI_002 *	S	74	H	LEC_GALNI	---	---	A	S	51	H
2	UniProt	VAR_LEC_GALNI_003 *	F	76	Y	LEC_GALNI	---	---	A	F	53	Y
3	UniProt	VAR_LEC_GALNI_004 *	C	109	S	LEC_GALNI	---	---	A	C	86	S
	* ID not provided by source

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

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	LEC_GALNI	24-132	1	A:1-108

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	LEC_GALNI	24-132	4	A:1-108

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	LEC_GALNI	24-132	4	A:1-108

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:PROTEIN  Length:108
 aligned with LEC_GALNI | P30617 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    33        43        53        63        73        83        93       103       113       123        
            LEC_GALNI    24 DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQNGNYVCILQKDRNVVIYGTDRWATGTHT 131
               SCOP domains d1jpca_ A: Lectin (agglutinin)                                                                               SCOP domains
               CATH domains 1jpcA00 A:1-108 Agglutinin, subunit A                                                                        CATH domains
               Pfam domains -B_lectin-1jpcA01 A:2-108                                                                                    Pfam domains
         Sec.struct. author ..eee.........eeee..eeeee.....eeeee.................eee.......eee.....eeee..........eeee.....eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------H-Y--------------------------------S---------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: A:1-108 UniProt: 24-132                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1jpc A   1 DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQNGNYVCILQKDRNVVIYGTDRWATGTHT 108
                                    10        20        30        40        50        60        70        80        90       100

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Classification and Annotation

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Pfam Domains (1, 1)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A (LEC_GALNI | P30617)

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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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