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(-) Description

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)

(-) Compounds

Molecule 1 - PROTEIN (PEANUT LECTIN)
    ChainsA, B, C, D
    Organism CommonPEANUT
    Organism ScientificARACHIS HYPOGAEA
    Organism Taxid3818
    SynonymPEANUT AGGLUTININ-C-LACTOSE COMPLEX

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MBG4Ligand/IonMETHYL-BETA-GALACTOSE
3MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP 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:532BINDING SITE FOR RESIDUE MBG A 439
02AC2SOFTWAREASP B:80 , ASP B:83 , GLY B:103 , GLY B:104 , ASN B:127 , SER B:211 , HOH B:519 , HOH B:555BINDING SITE FOR RESIDUE MBG B 440
03AC3SOFTWAREASP C:80 , ASP C:83 , GLY C:103 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211BINDING SITE FOR RESIDUE MBG C 441
04AC4SOFTWAREASP 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:491BINDING SITE FOR RESIDUE MBG D 442
05AC5SOFTWAREASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:525 , HOH A:526BINDING SITE FOR RESIDUE CA A 437
06AC6SOFTWAREGLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:527 , HOH A:528BINDING SITE FOR RESIDUE MN A 238
07AC7SOFTWAREASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , MN B:238 , HOH B:551 , HOH B:552BINDING SITE FOR RESIDUE CA B 237
08AC8SOFTWAREGLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , CA B:237 , HOH B:553 , HOH B:554BINDING SITE FOR RESIDUE MN B 238
09AC9SOFTWAREASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:516 , HOH C:517BINDING SITE FOR RESIDUE CA C 237
10BC1SOFTWAREGLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:518 , HOH C:519BINDING SITE FOR RESIDUE MN C 238
11BC2SOFTWAREASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:523 , HOH D:524BINDING SITE FOR RESIDUE CA D 237
12BC3SOFTWAREGLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:525 , HOH D:526BINDING SITE FOR RESIDUE MN D 238

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 12)

Asymmetric/Biological Unit (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LECG_ARAHY_001 *E115VLECG_ARAHY  ---  ---A/B/C/DE92V
2UniProtVAR_LECG_ARAHY_002 *K172ALECG_ARAHY  ---  ---A/B/C/DK149A
3UniProtVAR_LECG_ARAHY_003 *K185ILECG_ARAHY  ---  ---A/B/C/DK162I
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECG_ARAHY141-147
 
 
 
  4A:118-124
B:118-124
C:118-124
D:118-124
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECG_ARAHY221-230
 
 
 
  4A:198-207
B:198-207
C:198-207
D:198-207

(-) Exons   (0, 0)

(no "Exon" information available for 1QF3)

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (2, 2)

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.

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    Ala A:82 - Asp A:83   [ RasMol ]  
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    Ala D:82 - Asp D:83   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LECG_ARAHY | P028721bzw 1ciw 1cq9 1cr7 1rir 1rit 1v6i 1v6j 1v6k 1v6l 1v6m 1v6n 1v6o 2dh1 2dv9 2dva 2dvb 2dvd 2dvf 2dvg 2pel 2tep

(-) Related Entries Specified in the PDB File

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