3IPV - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SPATHOLOBUS PARVIFLORUS SEED LECTIN

Authors :   K. Geethanandan, S. R. Bharath, J. Abhilash, C. Sadasivan, M. Haridas

Date :   18 Aug 09 (Deposition) - 08 Sep 09 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Galactose Binding, Seed Lectin, Hemagglutinin, Legume Lectin, Anti Fungal, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Geethanandan, J. Abhilash, S. R. Bharath, C. Sadasivan, M. Haridas
X-Ray Structure Of A Galactose-Specific Lectin From Spatholobous Parviflorous
Int. J. Biol. Macromol. V. 49 992 2011
PubMed-ID: 21889532 | Reference-DOI: 10.1016/J.IJBIOMAC.2011.08.021

Molecule 1 - LECTIN ALPHA CHAIN
	Chains	:	A, C
	Organism Scientific	:	SPATHOLOBUS PARVIFLORUS
	Organism Taxid	:	132465

Molecule 2 - LECTIN BETA CHAIN
	Chains	:	B, D
	Organism Scientific	:	SPATHOLOBUS PARVIFLORUS
	Organism Taxid	:	132465

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:128 , TYR A:130 , ASN A:132 , ASP A:137 , HOH A:314 , HOH A:321	BINDING SITE FOR RESIDUE CA A 252
2	AC2	SOFTWARE	GLU A:126 , ASP A:128 , ASP A:137 , HIS A:142 , HOH A:332 , HOH A:333	BINDING SITE FOR RESIDUE MN A 253
3	AC3	SOFTWARE	ASP B:128 , TYR B:130 , ASN B:132 , ASP B:137 , HOH B:295 , HOH B:527	BINDING SITE FOR RESIDUE CA B 240
4	AC4	SOFTWARE	GLU B:126 , ASP B:128 , ASP B:137 , HIS B:142 , HOH B:291 , HOH B:609	BINDING SITE FOR RESIDUE MN B 241
5	AC5	SOFTWARE	ASP C:128 , TYR C:130 , ASN C:132 , ASP C:137 , HOH C:310 , HOH C:316	BINDING SITE FOR RESIDUE CA C 252
6	AC6	SOFTWARE	GLU C:126 , ASP C:128 , ASP C:137 , HIS C:142 , HOH C:266 , HOH C:677	BINDING SITE FOR RESIDUE MN C 253
7	AC7	SOFTWARE	ASP D:128 , TYR D:130 , ASN D:132 , ASP D:137 , HOH D:307 , HOH D:321	BINDING SITE FOR RESIDUE CA D 240
8	AC8	SOFTWARE	GLU D:126 , ASP D:128 , ASP D:137 , HIS D:142 , HOH D:287 , HOH D:551	BINDING SITE FOR RESIDUE MN D 241

(no "SS Bond" information available for 3IPV)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:87	-	Asp A:88
2	Ala B:87	-	Asp B:88
3	Ala C:87	-	Asp C:88
4	Ala D:87	-	Asp D:88

(no "SAP(SNP)/Variant" information available for 3IPV)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECB_SPAPA	123-129	2	B:123-129 D:123-129
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECA_SPAPA	123-129	2	A:123-129 C:123-129
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECB_SPAPA	204-213	2	B:204-213 D:204-213
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECA_SPAPA	204-213	2	A:204-213 C:204-213

(no "Exon" information available for 3IPV)

Asymmetric/Biological 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:249
 aligned with LECA_SPAPA | P86352 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           LECA_SPAPA     1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDKNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVSGSTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASGGKIETHDVFSWSFASKLAGXXTKDSSFLDGG 251
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ipvA00 A:1-251  [code=2.60.120.200, no name defined]                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee..............eeeeee...ee..........eeeeeeeee..........eeeeeeeee.......hhhhh..............eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeee.....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee..--.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG-------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipv A   1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDKNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVSGSTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASGGKIETHDVFSWSFASKLAG--TKDSSFLDGG 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |- |     250 
                                                                                                                                                                                                                                                                        239  |         
                                                                                                                                                                                                                                                                           242

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with LECB_SPAPA | P86353 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           LECB_SPAPA     1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDSNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVGDTTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASKGYIETHDVFSWSFASKLAG 239
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ipvB00 B:1-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee..............eeeeee...ee..........eeeeeeeee..........eeeeeeeee.......hhhhh........hhhhh.eeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG-------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipv B   1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDSNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVGDTTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASKGYIETHDVFSWSFASKLAG 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:249
 aligned with LECA_SPAPA | P86352 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           LECA_SPAPA     1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDKNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVSGSTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASGGKIETHDVFSWSFASKLAGXXTKDSSFLDGG 251
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ipvC00 C:1-251  [code=2.60.120.200, no name defined]                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee..............eeeeee...ee..........eeeeeeeee..........eeeeeeeee.......hhhhh........hhhhh.eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee..--.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG-------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipv C   1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDKNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVSGSTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASGGKIETHDVFSWSFASKLAG--TKDSSFLDGG 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |- |     250 
                                                                                                                                                                                                                                                                        239  |         
                                                                                                                                                                                                                                                                           242

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with LECB_SPAPA | P86353 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           LECB_SPAPA     1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDSNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVGDTTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASKGYIETHDVFSWSFASKLAG 239
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ipvD00 D:1-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee..............eeeeee...ee..........eeeeeeeee..........eeeeeeee........hhhhh........hhhhh.eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG-------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipv D   1 AEETSFVFSKFKPLEPNLILQGDALVTVAGVLQLTNVDSNGVPEPSSLGRATYSAPINIWDSATGLVASFATSFRFTIYAPNIATIADGLAFFLAPVASAPDSGGGFLGLFDSAVGDTTYQTVAVEFDTYENTVFTDPPYTHIGFDVNSISSIKTVKWSLANGEAAKVLITYNSAVKLLVASLVYPSSKTSFILADIVDLSSVLPEWVRVGFSAATGASKGYIETHDVFSWSFASKLAG 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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 '\|'

(no "SCOP Domain" information available for 3IPV)

Asymmetric/Biological 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)

Spatholobus parviflorus. Organism_taxid: 132465. (1)

1a	3ipvB00	B:1-239
1b	3ipvD00	D:1-239
1c	3ipvA00	A:1-251
1d	3ipvC00	C:1-251

(no "Pfam Domain" information available for 3IPV)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (LECA_SPAPA | P86352)

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:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.

Chain B,D (LECB_SPAPA | P86353)

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:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:87 - Asp A:88	[ RasMol ]
		Ala B:87 - Asp B:88	[ RasMol ]
		Ala C:87 - Asp C:88	[ RasMol ]
		Ala D:87 - Asp D:88	[ RasMol ]

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	3ipv
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(no "Related Entries Specified in the PDB File" available for 3IPV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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