1NIV - JenaLib

Title :   MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1, 3-METHYL-D-MANNOSE

Authors :   C. S. Wright, G. Hester

Date :   15 Mar 96 (Deposition) - 14 Oct 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

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

Reference :   G. Hester, C. S. Wright
The Mannose-Specific Bulb Lectin From Galanthus Nivalis (Snowdrop) Binds Mono- And Dimannosides At Distinct Sites. Structure Analysis Of Refined Complexes At 2. 3 A And 3. 0 A Resolution.
J. Mol. Biol. V. 262 516 1996
PubMed-ID: 8893860 | Reference-DOI: 10.1006/JMBI.1996.0532
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:89 , ASP A:91 , ASN A:93 , VAL A:95 , TYR A:97 , ASN C:83 , ASP C:100 , HIS C:107	BINDING SITE FOR RESIDUE MDM A 110
2	AC2	SOFTWARE	PRO A:39 , TRP A:41 , ASN A:44 , GLN A:57 , ASP A:59 , ASN A:61 , TYR A:65	BINDING SITE FOR RESIDUE MDM A 111
3	AC3	SOFTWARE	GLN A:26 , ASP A:28 , ASN A:30 , TYR A:34 , ASP A:37	BINDING SITE FOR RESIDUE MDM A 112
4	AC4	SOFTWARE	ASN A:83 , ASP A:100 , ALA A:103 , GLN C:89 , ASP C:91 , ASN C:93 , VAL C:95 , TYR C:97	BINDING SITE FOR RESIDUE MDM C 110
5	AC5	SOFTWARE	GLN C:57 , ASP C:59 , ASN C:61 , TYR C:65	BINDING SITE FOR RESIDUE MDM C 111
6	AC6	SOFTWARE	GLN C:26 , ASP C:28 , ASN C:30 , TYR C:34 , ASP C:37	BINDING SITE FOR RESIDUE MDM C 112

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric Unit (3, 6)

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

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

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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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 d1niva_ A: Lectin (agglutinin)                                                                               SCOP domains
               CATH domains 1nivA00 A:1-108 Agglutinin, subunit A                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....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
                 1niv A   1 DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQNGNYVCILQKDRNVVIYGTDRWATGTHT 108
                                    10        20        30        40        50        60        70        80        90       100

Chain C 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 d1nivc_ C: Lectin (agglutinin)                                                                               SCOP domains
               CATH domains 1nivC00 C:1-108 Agglutinin, subunit A                                                                        CATH domains
           Pfam domains (1) -B_lectin-1nivC01 C:2-108                                                                                    Pfam domains (1)
           Pfam domains (2) -B_lectin-1nivC02 C:2-108                                                                                    Pfam domains (2)
         Sec.struct. author ..eee..eee....eeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..........eeee.....eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------H-Y--------------------------------S---------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: C:1-108 UniProt: 24-132                                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1niv C   1 DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQNGNYVCILQKDRNVVIYGTDRWATGTHT 108
                                    10        20        30        40        50        60        70        80        90       100

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Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A,C (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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