Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  WINGED BEAN LECTIN, SACCHARIDE FREE FORM
 
Authors :  N. Manoj, V. R. Srinivas, K. Suguna
Date :  16 Dec 98  (Deposition) - 22 Dec 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lectin (Agglutinin), Legume Lectin, Protein Crystallography, Blood Group Specificity, Saccharide Free Form, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Manoj, V. R. Srinivas, K. Suguna
Structure Of Basic Winged-Bean Lectin And A Comparison With Its Saccharide-Bound Form.
Acta Crystallogr. , Sect. D V. 55 794 1999
PubMed-ID: 10089310  |  Reference-DOI: 10.1107/S090744499900044X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (AGGLUTININ)
    Chains: A, B
    Organism Common: WINGED BEAN
    Organism Scientific: PSOPHOCARPUS TETRAGONOLOBUS
    Organism Taxid: 3891
    Synonym: WINGED BEAN BASIC AGGLUTININ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MN2Ligand/IonMANGANESE (II) ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:82 , GLN A:217 , ASN A:219BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWAREARG B:82 , GLN B:217 , ASN B:219BINDING SITE FOR RESIDUE NAG B 501
3AC3SOFTWAREARG A:21 , ASN A:44 , PRO A:213BINDING SITE FOR RESIDUE NAG A 601
4AC4SOFTWAREASN B:44 , PRO B:213BINDING SITE FOR RESIDUE NAG B 601
5AC5SOFTWAREGLU A:122 , ASP A:124 , ASP A:131 , HIS A:136 , HOH A:663 , HOH A:664BINDING SITE FOR RESIDUE MN A 300
6AC6SOFTWAREASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:665 , HOH A:666BINDING SITE FOR RESIDUE CA A 303
7AC7SOFTWAREGLU B:122 , ASP B:124 , ASP B:131 , HIS B:136 , HOH B:678 , HOH B:679BINDING SITE FOR RESIDUE MN B 300
8AC8SOFTWAREASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:680 , HOH B:681BINDING SITE FOR RESIDUE CA B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WBF)

(-) 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: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 d1wbfa_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wbfA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee........................eeeeee...............eeeeeeeee...........eeeeeeeee........hhh...........eeeeeee..........eeeeeee......eeeee.......eeeeeeee....eeeeeeee....eeeeeeee..hhhh....eeeeeeeee..hhh.........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbf 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 d1wbfb_ B: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1wbfB00 B:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) Lectin_legB-1wbfB01 B:1-232                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) Lectin_legB-1wbfB02 B:1-232                                                                                                                                                                                                             ----- Pfam domains (2)
         Sec.struct. author .eeeeee.........eeeee........................eeeeee...............eeeeeeeee...........eeeeeeeee........hhh.....hhh...eeeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee..hhhh....eeeeeeeee..hhh.........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wbf 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
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:86 - Asp A:87   [ RasMol ]  
    Ala B:86 - Asp B:87   [ RasMol ]  
    Arg A:82 - Pro A:83   [ RasMol ]  
    Arg B:82 - Pro B:83   [ RasMol ]  
    Ile A:134 - Pro A:135   [ RasMol ]  
    Ile B:134 - Pro B:135   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wbf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LEC1_PSOTE | O24313
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LEC1_PSOTE | O24313
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LEC1_PSOTE | O24313: 1wbl 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 1WBF)