1QF3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PEANUT LECTIN COMPLEXED WITH METHYL-BETA-GALACTOSE

Authors :   R. Ravishankar, K. Suguna, A. Surolia, M. Vijayan

Date :   06 Apr 99 (Deposition) - 27 Jul 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Lectin, Legume Lectin, Water Bridges, Carbohydrate Specificity, Methyl-Beta- Galactose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Ravishankar, K. Suguna, A. Surolia, M. Vijayan
Structures Of The Complexes Of Peanut Lectin With Methyl-Beta-Galactose And N-Acetyllactosamine And A Comparative Study Of Carbohydrate Binding In Gal/Galnac-Specific Legume Lectins.
Acta Crystallogr. , Sect. D V. 55 1375 1999
PubMed-ID: 10417405 | Reference-DOI: 10.1107/S0907444999006587
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PEANUT LECTIN)
	Chains	:	A, B, C, D
	Organism Common	:	PEANUT
	Organism Scientific	:	ARACHIS HYPOGAEA
	Organism Taxid	:	3818
	Synonym	:	PEANUT AGGLUTININ-C-LACTOSE COMPLEX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MBG	4	Ligand/Ion	METHYL-BETA-GALACTOSE
3	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:80 , ASP A:83 , GLY A:104 , TYR A:125 , ASN A:127 , SER A:211 , HOH A:495 , HOH A:500 , HOH A:532	BINDING SITE FOR RESIDUE MBG A 439
02	AC2	SOFTWARE	ASP B:80 , ASP B:83 , GLY B:103 , GLY B:104 , ASN B:127 , SER B:211 , HOH B:519 , HOH B:555	BINDING SITE FOR RESIDUE MBG B 440
03	AC3	SOFTWARE	ASP C:80 , ASP C:83 , GLY C:103 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211	BINDING SITE FOR RESIDUE MBG C 441
04	AC4	SOFTWARE	ASP D:80 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , HOH D:467 , HOH D:491	BINDING SITE FOR RESIDUE MBG D 442
05	AC5	SOFTWARE	ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:525 , HOH A:526	BINDING SITE FOR RESIDUE CA A 437
06	AC6	SOFTWARE	GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:527 , HOH A:528	BINDING SITE FOR RESIDUE MN A 238
07	AC7	SOFTWARE	ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , MN B:238 , HOH B:551 , HOH B:552	BINDING SITE FOR RESIDUE CA B 237
08	AC8	SOFTWARE	GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , CA B:237 , HOH B:553 , HOH B:554	BINDING SITE FOR RESIDUE MN B 238
09	AC9	SOFTWARE	ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:516 , HOH C:517	BINDING SITE FOR RESIDUE CA C 237
10	BC1	SOFTWARE	GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:518 , HOH C:519	BINDING SITE FOR RESIDUE MN C 238
11	BC2	SOFTWARE	ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:523 , HOH D:524	BINDING SITE FOR RESIDUE CA D 237
12	BC3	SOFTWARE	GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:525 , HOH D:526	BINDING SITE FOR RESIDUE MN D 238

(no "SS Bond" information available for 1QF3)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:82	-	Asp A:83
2	Ala B:82	-	Asp B:83
3	Ala C:82	-	Asp C:83
4	Ala D:82	-	Asp D:83

Asymmetric/Biological 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)

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.	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

(no "Exon" information available for 1QF3)

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: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 d1qf3a_ A: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qf3A00 A:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee....................eeeeee...............eeeeeeeeeee.........eeeeeeee...........hhh............eeeeee....hhh......eeeeee......eeee......eeeeeeeeee....eeeeeee.....eeeeeee..hhhh....eeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf3 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 d1qf3b_ B: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qf3B00 B:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee....................eeeeee...............eeeeeeeeeeee........eeeeeeee...........hhh............eeeeee....hhh......eeeeee......eeee......eeeeeeeeee....eeeeeee.....eeeeeee..hhhh....eeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf3 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 d1qf3c_ C: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qf3C00 C:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee....................eeeeee...............eeeeeeeeeee.........eeeeeeee...........hhh............eeeeee....hhh......eeeeee......eeee......eeeeeeeeee....eeeeeee.....eeeeeee..hhhh....eeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf3 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 d1qf3d_ D: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qf3D00 D:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
           Pfam domains (1) -Lectin_legB-1qf3D01 D:2-226                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -Lectin_legB-1qf3D02 D:2-226                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) -Lectin_legB-1qf3D03 D:2-226                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) -Lectin_legB-1qf3D04 D:2-226                                                                                                                                                                                                      ------ Pfam domains (4)
         Sec.struct. author .eeeeeee.........eeeee....................eeeeee...............eeeeeeeeeeee........eeeeeeee...........hhh............eeeeee....hhh......eeeeee......eeee......eeeeeeeeee....eeeeeee.....eeeeeee..hhhh....eeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf3 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/Biological 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	d1qf3a_	A:
1b	d1qf3b_	B:
1c	d1qf3c_	C:
1d	d1qf3d_	D:

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)

Peanut (Arachis hypogaea) (22)

1a	1qf3A00	A:1-232
1b	1qf3B00	B:1-232
1c	1qf3C00	C:1-232
1d	1qf3D00	D:1-232

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Lectin_legB (93)

Arachis hypogaea (Peanut) (11)

1a	Lectin_legB-1qf3D01	D:2-226
1b	Lectin_legB-1qf3D02	D:2-226
1c	Lectin_legB-1qf3D03	D:2-226
1d	Lectin_legB-1qf3D04	D:2-226

Asymmetric/Biological 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/Biological Unit
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	Cis Peptide Bonds
		Ala A:82 - Asp A:83	[ RasMol ]
		Ala B:82 - Asp B:83	[ RasMol ]
		Ala C:82 - Asp C:83	[ RasMol ]
		Ala D:82 - Asp D:83	[ RasMol ]

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	1qf3
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(no "Related Entries Specified in the PDB File" available for 1QF3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

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Exons (0, 0)

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