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(-) Description

Title :  WINGED BEAN LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE
 
Authors :  M. M. Prabu, R. Sankaranarayanan, K. D. Puri, V. Sharma, A. Surolia, M. V K. Suguna
Date :  04 Apr 97  (Deposition) - 08 Apr 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Legume Lectin, Glycosylated Protein, Blood Group Specificity, Quaternary Association, Agglutinin, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Prabu, R. Sankaranarayanan, K. D. Puri, V. Sharma, A. Surolia, M. Vijayan, K. Suguna
Carbohydrate Specificity And Quaternary Association In Basi Winged Bean Lectin: X-Ray Analysis Of The Lectin At 2. 5 A Resolution.
J. Mol. Biol. V. 276 787 1998
PubMed-ID: 9500920  |  Reference-DOI: 10.1006/JMBI.1997.1568
(for further references see the PDB file header)

(-) Compounds

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

 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  (5, 31)

Asymmetric Unit (5, 31)
No.NameCountTypeFull Name
1AMG4Ligand/IonALPHA-METHYL-D-GALACTOSIDE
2CA4Ligand/IonCALCIUM ION
3FUC5Ligand/IonALPHA-L-FUCOSE
4MN4Ligand/IonMANGANESE (II) ION
5NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1AMG2Ligand/IonALPHA-METHYL-D-GALACTOSIDE
2CA-1Ligand/IonCALCIUM ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MN-1Ligand/IonMANGANESE (II) ION
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1AMG2Ligand/IonALPHA-METHYL-D-GALACTOSIDE
2CA-1Ligand/IonCALCIUM ION
3FUC3Ligand/IonALPHA-L-FUCOSE
4MN-1Ligand/IonMANGANESE (II) ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:80 , PRO A:83 , GLN A:217 , ASN A:219 , FUC A:502 , NAG A:503BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARENAG A:501 , NAG A:503 , ASN D:8 , GLN D:9BINDING SITE FOR RESIDUE FUC A 502
03AC3SOFTWARENAG A:501 , FUC A:502 , LYS D:53BINDING SITE FOR RESIDUE NAG A 503
04AC4SOFTWAREASN A:44 , NAG A:603 , THR D:61BINDING SITE FOR RESIDUE NAG A 601
05AC5SOFTWARENAG A:601 , HOH A:701BINDING SITE FOR RESIDUE NAG A 603
06AC6SOFTWAREARG B:82 , PRO B:83 , GLN B:217 , ASN B:219 , NAG B:503BINDING SITE FOR RESIDUE NAG B 501
07AC7SOFTWAREARG B:82 , NAG B:501 , HOH B:635BINDING SITE FOR RESIDUE NAG B 503
08AC8SOFTWARETRP B:43 , ASN B:44 , FUC B:602 , NAG B:603 , LEU D:113BINDING SITE FOR RESIDUE NAG B 601
09AC9SOFTWARENAG B:601 , NAG B:603 , LEU D:113 , SER D:114BINDING SITE FOR RESIDUE FUC B 602
10BC1SOFTWARENAG B:601 , FUC B:602 , HOH B:675BINDING SITE FOR RESIDUE NAG B 603
11BC2SOFTWAREGLN C:217 , ASN C:219 , FUC C:502 , NAG C:503 , HOH C:631BINDING SITE FOR RESIDUE NAG C 501
12BC3SOFTWAREHOH B:720 , NAG C:501 , NAG C:503BINDING SITE FOR RESIDUE FUC C 502
13BC4SOFTWARESER B:181 , NAG C:501 , FUC C:502 , HOH C:533BINDING SITE FOR RESIDUE NAG C 503
14BC5SOFTWAREPHE D:80 , PRO D:83 , LYS D:216 , GLN D:217 , ASN D:219 , FUC D:502 , NAG D:503 , HOH D:719BINDING SITE FOR RESIDUE NAG D 501
15BC6SOFTWAREARG D:82 , SER D:214 , NAG D:501 , NAG D:503BINDING SITE FOR RESIDUE FUC D 502
16BC7SOFTWAREARG D:82 , NAG D:501 , FUC D:502BINDING SITE FOR RESIDUE NAG D 503
17BC8SOFTWAREASN D:44 , PRO D:213 , FUC D:602 , NAG D:603BINDING SITE FOR RESIDUE NAG D 601
18BC9SOFTWARENAG D:601 , NAG D:603 , HOH D:632BINDING SITE FOR RESIDUE FUC D 602
19CC1SOFTWARENAG D:601 , FUC D:602 , HOH D:628 , HOH D:690BINDING SITE FOR RESIDUE NAG D 603
20CC2SOFTWAREHIS A:84 , ASP A:87 , GLY A:104 , GLY A:105 , PHE A:126 , ASN A:128 , GLY A:211 , ASP A:212 , ALA A:220 , HOH A:619 , HOH A:652BINDING SITE FOR RESIDUE AMG A 400
21CC3SOFTWAREHIS 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:623BINDING SITE FOR RESIDUE AMG B 400
22CC4SOFTWAREHIS 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:215 , ALA C:220 , HOH C:520BINDING SITE FOR RESIDUE AMG C 400
23CC5SOFTWAREARG D:82 , HIS D:84 , ASP D:87 , GLY D:104 , GLY D:105 , PHE D:126 , ASN D:128 , GLY D:211 , ASP D:212 , ALA D:220 , HOH D:619BINDING SITE FOR RESIDUE AMG D 400
24CC6SOFTWAREGLU A:122 , ASP A:124 , ASP A:131 , HIS A:136 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE MN A 300
25CC7SOFTWAREASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:606 , HOH A:607BINDING SITE FOR RESIDUE CA A 303
26CC8SOFTWAREGLU B:122 , ASP B:124 , ASP B:131 , HIS B:136 , HOH B:604 , HOH B:605BINDING SITE FOR RESIDUE MN B 300
27CC9SOFTWAREASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:606 , HOH B:607BINDING SITE FOR RESIDUE CA B 303
28DC1SOFTWAREGLU C:122 , ASP C:124 , ASP C:131 , HIS C:136 , SER C:146 , HOH C:504BINDING SITE FOR RESIDUE MN C 300
29DC2SOFTWAREASP C:124 , PHE C:126 , ASN C:128 , ASP C:131 , HOH C:505 , HOH C:506BINDING SITE FOR RESIDUE CA C 303
30DC3SOFTWAREGLU D:122 , ASP D:124 , ASP D:131 , HIS D:136 , HOH D:604 , HOH D:605BINDING SITE FOR RESIDUE MN D 300
31DC4SOFTWAREASP D:124 , PHE D:126 , ASN D:128 , ASP D:131 , HOH D:606BINDING SITE FOR RESIDUE CA D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:86 -Asp A:87
2Ile A:134 -Pro A:135
3Ala B:86 -Asp B:87
4Ile B:134 -Pro B:135
5Ala C:86 -Asp C:87
6Ile C:134 -Pro C:135
7Ala D:86 -Asp D:87
8Ile D:134 -Pro D:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WBL)

(-) 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 1WBL)

(-) 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 d1wbla_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wblA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeee.........eeeeee.eee...eeee...........eeeeeeee..............eeeeeeeeeee..........eeeeeee........hhhhh..........eeeeeeee.........eeeeeeee.....eeeee......eeeeeeeee....eeeeeee.......eeeeeeehhhhhh....eeeeeeee.hhhhh......eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbl 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 d1wblb_ B: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wblB00 B:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeee.........eeeeee.eee...eeee...........eeeeeeee..............eeeeeeeeeee..........eeeeeee........hhhhh..........eeeeeeee.........eeeeeeee.....eeeee......eeeeeeeee....eeeeeee.......eeeeeeehhhhhh....eeeeeeee.hhhhh......eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbl 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 d1wblc_ C: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wblC00 C:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeee.........eeeeee.eee...eeee...........eeeeeeee..............eeeeeeeeeee..........eeeeeee........hhhhh..........eeeeeeee.........eeeeeeee.....eeeee......eeeeeeeee....eeeeeee.hhhh..eeeeeeehhhhhh....eeeeeeee............eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbl 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 d1wbld_ D: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wblD00 D:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) Lectin_legB-1wblD01 D:1-232                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) Lectin_legB-1wblD02 D:1-232                                                                                                                                                                                                             ----- Pfam domains (2)
           Pfam domains (3) Lectin_legB-1wblD03 D:1-232                                                                                                                                                                                                             ----- Pfam domains (3)
           Pfam domains (4) Lectin_legB-1wblD04 D:1-232                                                                                                                                                                                                             ----- Pfam domains (4)
         Sec.struct. author eeeeeee.........eeeeee.eee...eeee...........eeeeeeee..............eeeeeeeeeee..........eeeeeee........hhhhh..........eeeeeeee.........eeeeeeee.....eeeee......eeeeeeeee....eeeeeee.......eeeeeeehhhhhh....eeeeeeee.hhhhh......eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbl 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  (1, 4)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) 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 2d3s 2dtw 2dty 2du0 2du1 2e51 2e53 2e7q 2e7t 2zmk 2zml 2zmn

(-) Related Entries Specified in the PDB File

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