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(-) Description

Title :  CRYSTAL STRUCTURE OF BASIC WINGED BEAN LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
 
Authors :  K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Date :  19 Jul 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Legume Lectin, Glycosylated Protein, Agglutinin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Structural Basis For The Carbohydrate-Specificity Of Basic Winged-Bean Lectin And Its Differential Affinity For Gal An Galnac
Acta Crystallogr. , Sect. D V. 62 1319 2006
PubMed-ID: 17057334  |  Reference-DOI: 10.1107/S0907444906028198
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BASIC AGGLUTININ
    Chains: A, B, C, D
    Organism Common: WINGED BEAN
    Organism Scientific: PSOPHOCARPUS TETRAGONOLOBUS
    Organism Taxid: 3891
    Synonym: WBA I

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 37)

Asymmetric Unit (7, 37)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3CA4Ligand/IonCALCIUM ION
4FUC7Ligand/IonALPHA-L-FUCOSE
5FUL1Ligand/IonBETA-L-FUCOSE
6MN4Ligand/IonMANGANESE (II) ION
7NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA-1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4FUC4Ligand/IonALPHA-L-FUCOSE
5FUL-1Ligand/IonBETA-L-FUCOSE
6MN-1Ligand/IonMANGANESE (II) ION
7NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (5, 15)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4FUC3Ligand/IonALPHA-L-FUCOSE
5FUL1Ligand/IonBETA-L-FUCOSE
6MN-1Ligand/IonMANGANESE (II) ION
7NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:84 , ASP A:87 , GLY A:104 , GLY A:105 , PHE A:126 , ASN A:128 , GLY A:211 , ASP A:212 , GLY A:215 , ALA A:220BINDING SITE FOR RESIDUE A2G A 1401
02AC2SOFTWAREARG A:82 , PRO A:83 , GLN A:217 , ASN A:219 , FUC A:502 , NAG A:503BINDING SITE FOR RESIDUE NAG A 501
03AC3SOFTWARENAG A:501 , NAG A:503 , ASN D:8 , GLN D:9BINDING SITE FOR RESIDUE FUC A 502
04AC4SOFTWARENAG A:501 , FUC A:502 , GLN D:9 , LYS D:53BINDING SITE FOR RESIDUE NAG A 503
05AC5SOFTWAREASN A:44 , PRO A:213 , FUC A:602 , NAG A:603BINDING SITE FOR RESIDUE NAG A 601
06AC6SOFTWARENAG A:601 , NAG A:603 , SER D:60BINDING SITE FOR RESIDUE FUC A 602
07AC7SOFTWARENAG A:601 , FUC A:602BINDING SITE FOR RESIDUE NAG A 603
08AC8SOFTWAREHIS B:84 , ASP B:87 , GLY B:104 , GLY B:105 , PHE B:126 , ASN B:128 , GLY B:211 , ASP B:212 , GLY B:215 , ALA B:220 , HOH B:2443 , HOH B:2447BINDING SITE FOR RESIDUE A2G B 2401
09AC9SOFTWARELEU A:113 , PHE B:80 , PRO B:83 , ASN B:219 , FUC B:502 , NAG B:503BINDING SITE FOR RESIDUE NAG B 501
10BC1SOFTWAREARG B:82 , NAG B:501 , NAG B:503BINDING SITE FOR RESIDUE FUC B 502
11BC2SOFTWAREARG B:82 , NAG B:501 , FUC B:502BINDING SITE FOR RESIDUE NAG B 503
12BC3SOFTWAREASN B:44 , FUC B:602 , NAG B:603 , HOH B:2423BINDING SITE FOR RESIDUE NAG B 601
13BC4SOFTWARENAG B:601 , NAG B:603 , LEU D:113 , SER D:114 , PRO D:115BINDING SITE FOR RESIDUE FUC B 602
14BC5SOFTWARENAG B:601 , FUC B:602BINDING SITE FOR RESIDUE NAG B 603
15BC6SOFTWAREHIS C:84 , ASP C:87 , GLY C:104 , GLY C:105 , PHE C:126 , ASN C:128 , GLY C:211 , ASP C:212 , GLY C:215BINDING SITE FOR RESIDUE A2G C 3401
16BC7SOFTWAREPHE C:80 , GLN C:217 , ASN C:219 , FUC C:502 , NAG C:503 , HOH C:3465BINDING SITE FOR RESIDUE NAG C 501
17BC8SOFTWARENAG C:501 , NAG C:503BINDING SITE FOR RESIDUE FUC C 502
18BC9SOFTWARESER B:181 , NAG C:501 , FUC C:502 , BMA C:504BINDING SITE FOR RESIDUE NAG C 503
19CC1SOFTWAREGLN B:56 , ASP B:59 , THR B:61 , GLU B:200 , NAG C:503BINDING SITE FOR RESIDUE BMA C 504
20CC2SOFTWAREASN C:44 , FUL C:602 , NAG C:603BINDING SITE FOR RESIDUE NAG C 601
21CC3SOFTWARENAG C:601 , NAG C:603BINDING SITE FOR RESIDUE FUL C 602
22CC4SOFTWARENAG C:601 , FUL C:602 , SER D:27BINDING SITE FOR RESIDUE NAG C 603
23CC5SOFTWAREHIS D:84 , ASP D:87 , GLY D:104 , GLY D:105 , PHE D:126 , ASN D:128 , GLY D:211 , ASP D:212 , GLY D:215 , HOH D:4437BINDING SITE FOR RESIDUE A2G D 4401
24CC6SOFTWAREPHE D:80 , GLN D:217 , ASN D:219 , FUC D:502 , NAG D:503BINDING SITE FOR RESIDUE NAG D 501
25CC7SOFTWARESER D:214 , NAG D:501 , NAG D:503BINDING SITE FOR RESIDUE FUC D 502
26CC8SOFTWARENAG D:501 , FUC D:502BINDING SITE FOR RESIDUE NAG D 503
27CC9SOFTWAREASN D:44 , FUC D:602 , NAG D:603BINDING SITE FOR RESIDUE NAG D 601
28DC1SOFTWARENAG D:601 , NAG D:603BINDING SITE FOR RESIDUE FUC D 602
29DC2SOFTWARENAG D:601 , FUC D:602BINDING SITE FOR RESIDUE NAG D 603
30DC3SOFTWAREGLU A:122 , ASP A:124 , ASP A:131 , HIS A:136 , HOH A:1402 , HOH A:1403BINDING SITE FOR RESIDUE MN A 1300
31DC4SOFTWAREASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:1404 , HOH A:1405BINDING SITE FOR RESIDUE CA A 1303
32DC5SOFTWAREGLU B:122 , ASP B:124 , ASP B:131 , HIS B:136 , HOH B:2402 , HOH B:2403BINDING SITE FOR RESIDUE MN B 2300
33DC6SOFTWAREASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:2404 , HOH B:2405BINDING SITE FOR RESIDUE CA B 2303
34DC7SOFTWAREGLU C:122 , ASP C:124 , ASP C:131 , HIS C:136 , HOH C:3402BINDING SITE FOR RESIDUE MN C 3300
35DC8SOFTWAREASP C:124 , PHE C:126 , ASN C:128 , ASP C:131 , HOH C:3403 , HOH C:3404BINDING SITE FOR RESIDUE CA C 3303
36DC9SOFTWAREGLU D:122 , ASP D:124 , ASP D:131 , HIS D:136 , HOH D:4402 , HOH D:4403BINDING SITE FOR RESIDUE MN D 4300
37EC1SOFTWAREASP D:124 , PHE D:126 , ASN D:128 , ASP D:131 , HOH D:4404BINDING SITE FOR RESIDUE CA D 4303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Arg A:82 -Pro A:83
2Ala A:86 -Asp A:87
3Ile A:134 -Pro A:135
4Arg B:82 -Pro B:83
5Ala B:86 -Asp B:87
6Ile B:134 -Pro B:135
7Arg C:82 -Pro C:83
8Ala C:86 -Asp C:87
9Ile C:134 -Pro C:135
10Arg D:82 -Pro D:83
11Ala D:86 -Asp D:87
12Ile D:134 -Pro D:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DTY)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC1_PSOTE120-126
 
 
 		  4A:119-125
B:119-125
C:119-125
D:119-125
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC1_PSOTE120-126
 
 
 		  2A:119-125
B:119-125
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC1_PSOTE120-126
 
 
 		  2-
-
C:119-125
D:119-125

(-) Exons   (0, 0)

(no "Exon" information available for 2DTY)

(-) Sequences/Alignments

Asymmetric 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:237
 aligned with LEC1_PSOTE | O24313 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           LEC1_PSOTE     2 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 238
               SCOP domains d2dtya_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 2dtyA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee...........eeeeeeee........hhhhh...........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee.hhhhh........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dty A   1 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 237
                                    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:237
 aligned with LEC1_PSOTE | O24313 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           LEC1_PSOTE     2 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 238
               SCOP domains d2dtyb_ B: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 2dtyB00 B:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee...........eeeeeeee........hhhhh...........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee.hhhhh........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dty B   1 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 237
                                    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:237
 aligned with LEC1_PSOTE | O24313 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           LEC1_PSOTE     2 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 238
               SCOP domains d2dtyc_ C: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 2dtyC00 C:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee...........eeeeeeee........hhhhh...........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee.hhhhh........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dty C   1 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 237
                                    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:237
 aligned with LEC1_PSOTE | O24313 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           LEC1_PSOTE     2 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 238
               SCOP domains d2dtyd_ D: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 2dtyD00 D:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee...........eeeeeeee........hhhhh...........eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee.hhhhh........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dty D   1 KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPG 237
                                    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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LEC1_PSOTE | O24313)
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.

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  LEC1_PSOTE | O24313
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  LEC1_PSOTE | O24313
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 Related Entries

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

UniProtKB/Swiss-Prot
        LEC1_PSOTE | O24313: 1wbf 1wbl 2d3s 2dtw 2du0 2du1 2e51 2e53 2e7q 2e7t 2zmk 2zml 2zmn

(-) Related Entries Specified in the PDB File

1wbf 1wbl 2d3s 2dtw 2du0 2du1