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(-) Description

Title :  PEANUT LECTIN COMPLEXED WITH T-ANTIGENIC DISACCHARIDE
 
Authors :  R. Ravishankar, M. Ravindran, K. Suguna, A. Surolia, M. Vijayan
Date :  05 Apr 99  (Deposition) - 08 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lectin, Legume Lectin, Water Bridges, Carbohydrate Specificity, T-Antigen, Protein Crystallography, Agglutinin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Ravishankar, M. Ravindran, K. Suguna, A. Surolia, M. Vijayan
The Specificity Of Peanut Agglutinin For Thomsen-Friedenreich Antigen Is Mediated By Water-Bridges
Curr. Sci. V. 72 855 1997
PubMed: search
(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-T-ANTIGEN COMPLEX

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GAL4Ligand/IonBETA-D-GALACTOSE
3MN4Ligand/IonMANGANESE (II) ION
4NGA4Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:80 , ALA A:82 , ASP A:83 , GLY A:104 , TYR A:125 , ASN A:127 , SER A:211 , NGA A:240 , HOH A:288 , HOH A:301BINDING SITE FOR RESIDUE GAL A 239
02AC2SOFTWARESER A:211 , LEU A:212 , GLY A:213 , GAL A:239 , HOH A:263 , HOH A:311 , HOH A:337 , HOH A:344 , NGA B:240BINDING SITE FOR RESIDUE NGA A 240
03AC3SOFTWAREASP B:80 , ALA B:82 , ASP B:83 , GLY B:103 , GLY B:104 , TYR B:125 , ASN B:127 , SER B:211 , NGA B:240 , HOH B:305BINDING SITE FOR RESIDUE GAL B 239
04AC4SOFTWARENGA A:240 , SER B:211 , LEU B:212 , GLY B:213 , GAL B:239 , HOH B:286 , HOH B:373BINDING SITE FOR RESIDUE NGA B 240
05AC5SOFTWAREASP C:80 , ALA C:82 , ASP C:83 , GLY C:103 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211 , NGA C:240 , HOH C:298 , HOH C:332 , HOH C:333BINDING SITE FOR RESIDUE GAL C 239
06AC6SOFTWARESER C:211 , LEU C:212 , GLY C:213 , GAL C:239 , HOH C:309 , HOH C:333BINDING SITE FOR RESIDUE NGA C 240
07AC7SOFTWAREASP D:80 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , NGA D:240 , HOH D:303BINDING SITE FOR RESIDUE GAL D 239
08AC8SOFTWARESER D:211 , LEU D:212 , GLY D:213 , GAL D:239 , HOH D:311BINDING SITE FOR RESIDUE NGA D 240
09AC9SOFTWAREASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:376 , HOH A:377BINDING SITE FOR RESIDUE CA A 237
10BC1SOFTWAREGLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:378 , HOH A:379BINDING SITE FOR RESIDUE MN A 238
11BC2SOFTWAREASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , HOH B:390 , HOH B:391BINDING SITE FOR RESIDUE CA B 237
12BC3SOFTWAREGLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , HOH B:392 , HOH B:393BINDING SITE FOR RESIDUE MN B 238
13BC4SOFTWAREASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:340 , HOH C:341BINDING SITE FOR RESIDUE CA C 237
14BC5SOFTWAREGLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:342BINDING SITE FOR RESIDUE MN C 238
15BC6SOFTWAREASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:360 , HOH D:361BINDING SITE FOR RESIDUE CA D 237
16BC7SOFTWAREGLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:362 , HOH D:363BINDING SITE FOR RESIDUE MN D 238

(-) SS Bonds  (0, 0)

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

(-) 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 2TEP)

(-) 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 d2tepa_ A: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2tepA00 A: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
                 2tep 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 d2tepb_ B: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2tepB00 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
                 2tep 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 d2tepc_ C: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2tepC00 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...........eeeeeee....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
                 2tep 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 d2tepd_ D: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2tepD00 D:1-232  [code=2.60.120.200, no name defined]                                                                                                                                                                                    CATH domains
           Pfam domains (1) -Lectin_legB-2tepD01 D:2-226                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -Lectin_legB-2tepD02 D:2-226                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) -Lectin_legB-2tepD03 D:2-226                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) -Lectin_legB-2tepD04 D:2-226                                                                                                                                                                                                      ------ Pfam domains (4)
         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
                 2tep 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)
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  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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  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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 Related Entries

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

UniProtKB/Swiss-Prot
        LECG_ARAHY | P028721bzw 1ciw 1cq9 1cr7 1qf3 1rir 1rit 1v6i 1v6j 1v6k 1v6l 1v6m 1v6n 1v6o 2dh1 2dv9 2dva 2dvb 2dvd 2dvf 2dvg 2pel

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2TEP)