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

(-) Description

Title :  WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE
 
Authors :  N. Manoj, V. R. Srinivas, A. Surolia, M. Vijayan, K. Suguna
Date :  11 Jul 00  (Deposition) - 11 Jul 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Legume Lectin, Glycosylated Protein, H-Antigenic Specificity, Agglutinin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Manoj, V. R. Srinivas, A. Surolia, M. Vijayan, K. Suguna
Carbohydrate Specificity And Salt-Bridge Mediated Conformational Change In Acidic Winged Bean Agglutinin.
J. Mol. Biol. V. 302 1129 2000
PubMed-ID: 11183779  |  Reference-DOI: 10.1006/JMBI.2000.4111
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACIDIC LECTIN
    Chains: A, B
    Organ: LEGUMINOUS SEEDS
    Organism Common: WINGED BEAN
    Organism Scientific: PSOPHOCARPUS TETRAGONOLOBUS
    Organism Taxid: 3891
    Synonym: ACIDIC AGGLUTININ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1AMG1Ligand/IonALPHA-METHYL-D-GALACTOSIDE
2CA2Ligand/IonCALCIUM ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4MN2Ligand/IonMANGANESE (II) ION
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:76 , THR A:78 , GLY A:158 , VAL A:160 , GLU A:224 , NAG A:503BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARETHR A:78 , NAG A:501 , MAN A:504BINDING SITE FOR RESIDUE NAG A 503
03AC3SOFTWARESER A:147 , NAG A:503BINDING SITE FOR RESIDUE MAN A 504
04AC4SOFTWAREASN B:76 , GLU B:224 , NAG B:503BINDING SITE FOR RESIDUE NAG B 501
05AC5SOFTWARENAG B:501 , MAN B:504BINDING SITE FOR RESIDUE NAG B 503
06AC6SOFTWARENAG B:503BINDING SITE FOR RESIDUE MAN B 504
07AC7SOFTWARETYR A:83 , ASP A:88 , GLY A:106 , PHE A:127 , ASN A:129 , GLY A:214 , TYR A:215 , GLN A:216 , HOH A:512BINDING SITE FOR RESIDUE AMG A 400
08AC8SOFTWAREGLU A:123 , ASP A:125 , ASP A:132 , HIS A:137 , HOH A:523 , HOH A:526BINDING SITE FOR RESIDUE MN A 300
09AC9SOFTWAREASP A:125 , PHE A:127 , ASN A:129 , ASP A:132 , HOH A:524 , HOH A:527BINDING SITE FOR RESIDUE CA A 302
10BC1SOFTWAREGLU B:123 , ASP B:125 , ASP B:132 , HIS B:137 , HOH B:517 , HOH B:518BINDING SITE FOR RESIDUE MN B 301
11BC2SOFTWAREASP B:125 , PHE B:127 , ASN B:129 , ASP B:132 , HOH B:519BINDING SITE FOR RESIDUE CA B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F9K)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Tyr A:83 -Pro A:84
2Ala A:87 -Asp A:88
3Val A:135 -Pro A:136
4Tyr B:83 -Pro B:84
5Ala B:87 -Asp B:88
6Val B:135 -Pro B:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F9K)

(-) Exons   (0, 0)

(no "Exon" information available for 1F9K)

(-) 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:234
 aligned with Q9SM56_PSOTE | Q9SM56 from UniProtKB/TrEMBL  Length:240

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
         Q9SM56_PSOTE     1 ETQSFNFDHFEENSKELNLQRQASIKSSGVLELTKLTKNGVPVWKSTGRALYAEPIKIWDSTTGNVASFETRFSFNITQPYAYPEPADGLTFFMVPPNSPGGEDGGNLGVFKPSNPEGDNALAVEFDTFQNTWDPQVPHIGIDVNSIVSSKTLHFQLENGGVANVVIKYDSPTKILNVVLAFHSVGTVYTLSNIVDLKQEFPNSEWVNVGLSATTGYQKNAVETHEIISWSFTSSL 236
               SCOP domains d1f9ka_ A: Legume lectin                                                                                                                                                                                                                     SCOP domains
               CATH domains 1f9kA00 A:1-234  [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..........eeeeeeeeeee.........eeeeeeee........hhhhh.....--......eeeeee...........eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh....eeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9k A   1 ETQSFNFDHFEENSKELNLQRQASIKSNGVLELTKLTKNGVPVWKSTGRALYAEPIKIWDSTTGNVASFETRFSFNITQPYAYPEPADGLTFFMVPPNSPQGEDGGNLGVFKP--PEGDNAFAVEFDTFQNTWDPQVPHIGIDVNSIVSSKTLHFQLENGGVANVVIKYDSPTKILNVVLAFHSVGTVYTLSNIVDLKQEFPNSEWVNVGLSATTGYQKNAVETHEIISWSFTSSL 234
                                    10        20        30        40        50        60        70        80        90       100       110  |  | 118       128       138       148       158       168       178       188       198       208       218       228      
                                                                                                                                          113  |                                                                                                                        
                                                                                                                                             114                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with Q9SM56_PSOTE | Q9SM56 from UniProtKB/TrEMBL  Length:240

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
         Q9SM56_PSOTE     1 ETQSFNFDHFEENSKELNLQRQASIKSSGVLELTKLTKNGVPVWKSTGRALYAEPIKIWDSTTGNVASFETRFSFNITQPYAYPEPADGLTFFMVPPNSPGGEDGGNLGVFKPSNPEGDNALAVEFDTFQNTWDPQVPHIGIDVNSIVSSKTLHFQLENGGVANVVIKYDSPTKILNVVLAFHSVGTVYTLSNIVDLKQEFPNSEWVNVGLSATTGYQKNAVETHEIISWSFTSSL 236
               SCOP domains d1f9kb_ B: Legume lectin                                                                                                                                                                                                                     SCOP domains
               CATH domains 1f9kB00 B:1-234  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee..ee.....ee....hhhhh.....eeeeee...ee..........eeeeeeeee...........eeeeeeee........hhhhh.....--......eeeeee...........eeeeee.......eee.......eeeeeeeee....eeeeeeee....eeeeeeee.hhhhhh....eeeeeeeeee..........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9k B   1 ETQSFNFDHFEENSKELNLQRQASIKSNGVLELTKLTKNGVPVWKSTGRALYAEPIKIWDSTTGNVASFETRFSFNITQPYAYPEPADGLTFFMVPPNSPQGEDGGNLGVFKP--PEGDNAFAVEFDTFQNTWDPQVPHIGIDVNSIVSSKTLHFQLENGGVANVVIKYDSPTKILNVVLAFHSVGTVYTLSNIVDLKQEFPNSEWVNVGLSATTGYQKNAVETHEIISWSFTSSL 234
                                    10        20        30        40        50        60        70        80        90       100       110  |  | 118       128       138       148       158       168       178       188       198       208       218       228      
                                                                                                                                          113  |                                                                                                                        
                                                                                                                                             114
   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  (0, 0)

(no "Pfam Domain" information available for 1F9K)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9SM56_PSOTE | Q9SM56)
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
    AMG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:87 - Asp A:88   [ RasMol ]  
    Ala B:87 - Asp B:88   [ RasMol ]  
    Tyr A:83 - Pro A:84   [ RasMol ]  
    Tyr B:83 - Pro B:84   [ RasMol ]  
    Val A:135 - Pro A:136   [ RasMol ]  
    Val B:135 - Pro B:136   [ 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
  1f9k
    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
  Q9SM56_PSOTE | Q9SM56
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9SM56_PSOTE | Q9SM56
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9SM56_PSOTE | Q9SM56: 1fay

(-) Related Entries Specified in the PDB File

1fay WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D- GALACTOSE (MONOCLINIC FORM)