2DH1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEANUT LECTIN LACTOSE-AZOBENZENE-4,4'-DICARBOXYLIC ACID-LACTOSE COMPLEX

Authors :   S. K. Natchiar, O. Srinivas, M. Nivedita, D. Sagarika, N. Jayaraman, A. Surolia, M. Vijayan

Date :   17 Mar 06 (Deposition) - 15 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   7.65

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

Keywords :   Legume Lectin, Agglutinin, Crosslink, Open Quaternary Structure, Carbohydrate Specificity, Multivalency, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Natchiar, O. Srinivas, M. Nivedita, D. Sagarika, N. Jayaraman, A. Surolia, M. Vijayan
Multivalency In Lectins - A Crystallographic, Modelling And Light-Scattering Study Involving Peanut Lectin And A Bivalent Ligand
Curr. Sci. V. 90 1230 2006
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GALACTOSE-BINDING LECTIN
	Chains	:	A, B, C, D
	Organism Common	:	PEANUT
	Organism Scientific	:	ARACHIS HYPOGAEA
	Organism Taxid	:	3818
	Synonym	:	AGGLUTININ, PNA

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DH1)

(no "Site" information available for 2DH1)

(no "SS Bond" information available for 2DH1)

(no "Cis Peptide Bond" information available for 2DH1)

Asymmetric Unit (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECG_ARAHY_001 *	E	115	V	LECG_ARAHY	---	---	A/B/C/D	E	92	V
2	UniProt	VAR_LECG_ARAHY_002 *	K	172	A	LECG_ARAHY	---	---	A/B/C/D	K	149	A
3	UniProt	VAR_LECG_ARAHY_003 *	K	185	I	LECG_ARAHY	---	---	A/B/C/D	K	162	I
	* 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_LECG_ARAHY_001 *	E	115	V	LECG_ARAHY	---	---	A/D	E	92	V
2	UniProt	VAR_LECG_ARAHY_002 *	K	172	A	LECG_ARAHY	---	---	A/D	K	149	A
3	UniProt	VAR_LECG_ARAHY_003 *	K	185	I	LECG_ARAHY	---	---	A/D	K	162	I
	* ID not provided by source

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

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LECG_ARAHY_001 *	E	115	V	LECG_ARAHY	---	---	B/C	E	92	V
2	UniProt	VAR_LECG_ARAHY_002 *	K	172	A	LECG_ARAHY	---	---	B/C	K	149	A
3	UniProt	VAR_LECG_ARAHY_003 *	K	185	I	LECG_ARAHY	---	---	B/C	K	162	I
	* ID not provided by source

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECG_ARAHY	141-147	4	A:118-124 B:118-124 C:118-124 D:118-124
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECG_ARAHY	221-230	4	A:198-207 B:198-207 C:198-207 D:198-207

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECG_ARAHY	141-147	2	A:118-124 - - D:118-124
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECG_ARAHY	221-230	2	A:198-207 - - D:198-207

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECG_ARAHY	141-147	2	- B:118-124 C:118-124 -
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECG_ARAHY	221-230	2	- B:198-207 C:198-207 -

(no "Exon" information available for 2DH1)

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:232
 aligned with LECG_ARAHY | P02872 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:232
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           LECG_ARAHY    24 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 255
               SCOP domains d2dh1a1 A:1-232 Legume lectin                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dh1 A   1 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with LECG_ARAHY | P02872 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:232
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           LECG_ARAHY    24 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 255
               SCOP domains d2dh1b1 B:1-232 Legume lectin                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dh1 B   1 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 232
                                    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:232
 aligned with LECG_ARAHY | P02872 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:232
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           LECG_ARAHY    24 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 255
               SCOP domains d2dh1c1 C:1-232 Legume lectin                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dh1 C   1 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain D from PDB  Type:PROTEIN  Length:232
 aligned with LECG_ARAHY | P02872 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:232
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           LECG_ARAHY    24 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 255
               SCOP domains d2dh1d1 D:1-232 Legume lectin                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dh1 D   1 AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITT 232
                                    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 '\|'

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)

Peanut (Arachis hypogaea) [TaxId: 3818] (23)

1a	d2dh1a1	A:1-232
1b	d2dh1b1	B:1-232
1c	d2dh1c1	C:1-232
1d	d2dh1d1	D:1-232

(no "CATH Domain" information available for 2DH1)

(no "Pfam Domain" information available for 2DH1)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LECG_ARAHY | P02872)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dh1)

	Sites
(no "Sites" information available for 2dh1)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dh1)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2dh1
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1v6i	PEANUT LECTIN-LACTOSE COMPLEX IN ACIDIC PH
2pel	PEANUT LECTIN-LACTOSE COMPLEX AT NEUTRAL PH
2tep	PEANUT LECTIN T-ANTIGEN COMPLEX AT NEUTRAL PH

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

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Gene Ontology (2, 2)

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