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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PEANUT LECTIN IN COMPLEX WITH MESO-TETRASULPHONATOPHENYLPORPHYRIN AND LACTOSE

Authors :   M. Goel, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke

Date :   17 Nov 03 (Deposition) - 28 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goel, R. S. Damai, D. K. Sethi, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke
Crystal Structures Of The Pna-Porphyrin Complex In The Presence And Absence Of Lactose: Mapping The Conformational Changes On Lactose Binding, Interacting Surfaces, And Supramolecular Aggregations.
Biochemistry V. 44 5588 2005
PubMed-ID: 15823017 | Reference-DOI: 10.1021/BI047377S
(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/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 21)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	LAT	2	Ligand/Ion	BETA-LACTOSE
3	MN	4	Ligand/Ion	MANGANESE (II) ION
4	SFP	11	Ligand/Ion	5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP C:80 , ASP C:83 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211 , LEU C:212 , GLY C:213 , GLY C:214 , HOH C:261	BINDING SITE FOR RESIDUE LAT C 246
02	AC2	SOFTWARE	ASP D:80 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , LEU D:212 , GLY D:213	BINDING SITE FOR RESIDUE LAT D 247
03	AC3	SOFTWARE	ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132	BINDING SITE FOR RESIDUE CA A 248
04	AC4	SOFTWARE	GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137	BINDING SITE FOR RESIDUE MN A 249
05	AC5	SOFTWARE	ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132	BINDING SITE FOR RESIDUE CA B 250
06	AC6	SOFTWARE	GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137	BINDING SITE FOR RESIDUE MN B 251
07	AC7	SOFTWARE	ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132	BINDING SITE FOR RESIDUE CA C 252
08	AC8	SOFTWARE	GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , SER C:147 , HOH C:256	BINDING SITE FOR RESIDUE MN C 253
09	AC9	SOFTWARE	ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132	BINDING SITE FOR RESIDUE CA D 254
10	BC1	SOFTWARE	GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , VAL D:145 , SER D:147	BINDING SITE FOR RESIDUE MN D 255
11	BC2	SOFTWARE	ARG A:215 , SFP A:243 , SFP A:251 , PRO D:134 , THR D:135	BINDING SITE FOR RESIDUE SFP A 250
12	BC3	SOFTWARE	ASN A:41 , SER A:100 , ILE A:101 , LEU A:212 , SFP A:250 , SFP C:240 , PRO D:134	BINDING SITE FOR RESIDUE SFP A 251
13	BC4	SOFTWARE	ASN B:38 , ARG B:215 , SFP B:238 , THR C:135	BINDING SITE FOR RESIDUE SFP B 237
14	BC5	SOFTWARE	ASN B:41 , ILE B:101 , LEU B:212 , SFP B:237 , PRO C:134 , SFP D:242	BINDING SITE FOR RESIDUE SFP B 238
15	BC6	SOFTWARE	ARG C:53 , SER C:56 , THR C:59 , THR C:231 , SFP C:240	BINDING SITE FOR RESIDUE SFP C 239
16	BC7	SOFTWARE	THR A:111 , LEU A:212 , SFP A:251 , ARG C:53 , ALA C:58 , SFP C:239 , HOH C:254	BINDING SITE FOR RESIDUE SFP C 240
17	BC8	SOFTWARE	ARG D:53 , SER D:56 , THR D:231 , SFP D:242 , HOH D:257	BINDING SITE FOR RESIDUE SFP D 241
18	BC9	SOFTWARE	THR B:111 , SFP B:238 , ARG D:53 , ALA D:58 , SFP D:241	BINDING SITE FOR RESIDUE SFP D 242
19	CC1	SOFTWARE	THR A:25 , LEU A:27 , ASN A:29 , ASN A:31 , GLN A:33 , LEU A:37 , ASN A:38 , GLU A:72 , ASP A:75 , TYR A:79 , ILE A:217 , LEU A:219 , ARG A:221 , SFP A:244 , SFP A:250 , HOH A:263	BINDING SITE FOR RESIDUE SFP A 243
20	CC2	SOFTWARE	SER A:28 , ASN A:29 , SFP A:243 , SER B:28 , ASN B:29 , LYS B:74 , SFP B:245	BINDING SITE FOR RESIDUE SFP A 244
21	CC3	SOFTWARE	SFP A:244 , THR B:25 , ASN B:29 , ASN B:31 , GLN B:33 , ASN B:38 , GLU B:72 , ASP B:75 , ILE B:217 , LEU B:219	BINDING SITE FOR RESIDUE SFP B 245

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

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 1RIT)

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 d1rita_ A: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ritA00 A:1-232  [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......................eeeeeeeeee...hhhhh.....eeeeeeee....eeee.......eeeeeeee.....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee.........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rit 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 d1ritb_ B: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ritB00 B:1-232  [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......................eeeeeeeeee...hhhhh.....eeeeeeee....eeee.......eeeeeeee.....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee.........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rit 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 d1ritc_ C: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ritC00 C:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.........eeeeee...ee..........eeeeeeeeeee.........eeeeeeee..........hhhhh.......eeeeeeeeee...hhhhh.....eeeeeeee....eeee......eeeeeeeeee....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rit 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 d1ritd_ D: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ritD00 D:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
           Pfam domains (1) -Lectin_legB-1ritD01 D:2-226                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -Lectin_legB-1ritD02 D:2-226                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) -Lectin_legB-1ritD03 D:2-226                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) -Lectin_legB-1ritD04 D:2-226                                                                                                                                                                                                      ------ Pfam domains (4)
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.........eeeeee...ee..........eeeeeeeeeeee........eeeeeeee..........hhhhh.......eeeeeeeeee...hhhhh.....eeeeeeee....eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee......eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rit 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	d1rita_	A:
1b	d1ritb_	B:
1c	d1ritc_	C:
1d	d1ritd_	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	1ritA00	A:1-232
1b	1ritB00	B:1-232
1c	1ritC00	C:1-232
1d	1ritD00	D:1-232

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Lectin_legB (93)

Arachis hypogaea (Peanut) (11)

1a	Lectin_legB-1ritD01	D:2-226
1b	Lectin_legB-1ritD02	D:2-226
1c	Lectin_legB-1ritD03	D:2-226
1d	Lectin_legB-1ritD04	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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	Ligands, Modified Residues, Ions
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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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	1rit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (21, 21)

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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