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(-) Description

Title :  CRYSTAL STRUCTURE OF PEANUT LECTIN GAL-BETA-1,3-GAL COMPLEX
 
Authors :  S. K. Natchiar, O. Srinivas, N. Mitra, A. Surolia, N. Jayaraman, M. Vijayan
Date :  30 Jul 06  (Deposition) - 07 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Legume Lectin, Agglutinin, Open Quaternary Structure, Carbohydrate Specificity, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Natchiar, O. Srinivas, N. Mitra, A. Surolia, N. Jayaraman, M. Vijayan
Structural Studies On Peanut Lectin Complexed With Disaccharides Involving Different Linkages: Further Insights Into The Structure And Interactions Of The Lectin
Acta Crystallogr. , Sect. D V. 62 1413 2006
PubMed-ID: 17057347  |  Reference-DOI: 10.1107/S0907444906035712
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALACTOSE-BINDING LECTIN
    Chains: A, B, C, D
    Fragment: RESIDUES 1-236
    Organism Common: PEANUT
    Organism Scientific: ARACHIS HYPOGAEA
    Organism Taxid: 3818
    Synonym: AGGLUTININ, PNA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GAL8Ligand/IonBETA-D-GALACTOSE
3MN4Ligand/IonMANGANESE (II) ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:80 , ALA A:82 , ASP A:83 , GLY A:103 , GLY A:104 , TYR A:125 , ASN A:127 , SER A:211 , GAL A:240 , HOH A:363 , HOH A:432BINDING SITE FOR RESIDUE GAL A 239
02AC2SOFTWARESER A:211 , LEU A:212 , GLY A:213 , GAL A:239 , HOH A:363 , GAL B:240BINDING SITE FOR RESIDUE GAL 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 , GAL B:240 , HOH B:1493BINDING SITE FOR RESIDUE GAL B 239
04AC4SOFTWAREGAL A:240 , SER B:211 , LEU B:212 , GLY B:213 , GAL B:239 , HOH B:1437BINDING SITE FOR RESIDUE GAL B 240
05AC5SOFTWAREASP C:80 , ASP C:83 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211 , GLY C:213 , GLY C:214 , GAL C:240 , HOH C:2394BINDING SITE FOR RESIDUE GAL C 239
06AC6SOFTWARESER C:211 , LEU C:212 , GLY C:213 , GAL C:239 , HOH C:2325BINDING SITE FOR RESIDUE GAL C 240
07AC7SOFTWAREASP D:80 , ALA D:82 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , GAL D:240 , HOH D:350BINDING SITE FOR RESIDUE GAL D 239
08AC8SOFTWARESER D:211 , LEU D:212 , GLY D:213 , GAL D:239BINDING SITE FOR RESIDUE GAL D 240
09AC9SOFTWAREASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:337 , HOH A:338BINDING SITE FOR RESIDUE CA A 237
10BC1SOFTWAREGLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:437 , HOH A:438BINDING SITE FOR RESIDUE MN A 238
11BC2SOFTWAREASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , HOH B:1392 , HOH B:1494BINDING SITE FOR RESIDUE CA B 237
12BC3SOFTWAREGLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , HOH B:1386 , HOH B:1393BINDING SITE FOR RESIDUE MN B 238
13BC4SOFTWAREASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:2332 , HOH C:2397BINDING SITE FOR RESIDUE CA C 237
14BC5SOFTWAREGLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:2395 , HOH C:2396BINDING SITE FOR RESIDUE MN C 238
15BC6SOFTWAREASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:352 , HOH D:353BINDING SITE FOR RESIDUE CA D 237
16BC7SOFTWAREGLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:354 , HOH D:355BINDING SITE FOR RESIDUE MN D 238
17BC8SOFTWAREHOH A:307 , ARG B:53 , SER B:56 , ALA B:58 , THR B:59 , THR B:231 , HOH B:1492BINDING SITE FOR RESIDUE SO4 B 1243
18BC9SOFTWAREARG C:53 , SER C:56 , ALA C:58 , THR C:59 , THR C:231 , HOH C:2261BINDING SITE FOR RESIDUE SO4 C 2243

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DV9)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Lys A:77 -Asp A:78
2Ala A:82 -Asp A:83
3Lys B:77 -Asp B:78
4Ala B:82 -Asp B:83
5Lys C:77 -Asp C:78
6Ala C:82 -Asp C:83
7Lys D:77 -Asp D:78
8Ala 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 2DV9)

(-) 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 d2dv9a_ A: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2dv9A00 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..........eeeeeeeeeee.........eeeeeeee..........hhhhh.......eeeeeeeeee...hhhhh.....eeeeeeee....eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dv9 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 d2dv9b_ B: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2dv9B00 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..........eeeeeeeeeee.........eeeeeeee..........hhhhh.......eeeeeeeeee...hhhhh.....eeeeeeee....eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dv9 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 d2dv9c_ C: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2dv9C00 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.......eeeeeeeee....eeeeee.......eeeeee.hhhhhh..eeeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------V--------------------------------------------------------A------------I---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dv9 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 d2dv9d_ D: Legume lectin                                                                                                                                                                                                                 SCOP domains
               CATH domains 2dv9D00 D: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
                 2dv9 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
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DV9)

(-) 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 ]  
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    Ala D:82 - Asp D:83   [ RasMol ]  
    Lys A:77 - Asp A:78   [ RasMol ]  
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  2dv9
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  LECG_ARAHY | P02872
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECG_ARAHY | P02872: 1bzw 1ciw 1cq9 1cr7 1qf3 1rir 1rit 1v6i 1v6j 1v6k 1v6l 1v6m 1v6n 1v6o 2dh1 2dva 2dvb 2dvd 2dvf 2dvg 2pel 2tep

(-) Related Entries Specified in the PDB File

1v6i PNA-LACTOSE COMPLEX AT LOW PH
1v6j PNA-LACTOSE COMPLEX, CRYSTALS WERE GROWN IN THE PRESENCE OF OLIGOPEPTIDE PVIWSSATG
1v6k PNA-LACTOSE COMPLEX, CRYSTALS WERE GROWN IN THE PRESENCE OF OLIGOPEPTIDE IWSSAGNVA
2dh1 PNA-LACTOSE-AZOBENZENE LACTOSE COMPLEX
2dva
2dvb
2dvd
2dvf
2dvg
2pel PNA-LACTOSE COMPLEX
2tep PNA-T-ANTIGEN COMPLEX