Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  A BARK LECTIN FROM ROBINIA PSEUDOACACIA IN COMPLEX WITH N-ACETYLGALACTOSAMINE
 
Authors :  A. Rabijns, C. Verboven, P. Rouge, A. Barre, E. J. Van Damme, W. J. Peumans, C. J. De Ranter
Date :  24 Aug 00  (Deposition) - 24 Aug 01  (Release) - 11 Mar 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Jelly Roll, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rabijns, C. Verboven, P. Rouge, A. Barre, E. J. Van Damme, W. J. Peumans, C. J. De Ranter
Structure Of A Legume Lectin From The Bark Of Robinia Pseudoacacia And Its Complex With N-Acetylgalactosamine
Proteins V. 44 470 2001
PubMed-ID: 11484224  |  Reference-DOI: 10.1002/PROT.1112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BARK AGGLUTININ I, POLYPEPTIDE A
    Chains: A
    Fragment: RESIDUES 32-268
    Organism Scientific: ROBINIA PSEUDOACACIA
    Organism Taxid: 35938
    Synonym: BARK LECTIN
    Tissue: BARK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA1Ligand/IonCALCIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:87 , GLY A:104 , GLY A:105 , ASN A:131 , GLY A:215 , ILE A:216 , ASP A:217 , TYR A:220 , HOH A:350BINDING SITE FOR RESIDUE A2G A 555
2AC2SOFTWAREASP A:127 , PHE A:129 , ASN A:131 , ASP A:135 , HOH A:267 , HOH A:268BINDING SITE FOR RESIDUE CA A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:86 -Asp A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LCB1_ROBPS153-159  1A:122-128
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LCB1_ROBPS233-242  1A:202-211
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LCB1_ROBPS153-159  4A:122-128
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LCB1_ROBPS233-242  4A:202-211

(-) Exons   (0, 0)

(no "Exon" information available for 1FNZ)

(-) 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:234
 aligned with LCB1_ROBPS | Q41159 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:237
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           LCB1_ROBPS    32 TGSLSFSFPKFAPNQPYLIFQRDALVTSTGVLQLTNVVNGVPSGKSLGRALYAAPFQIWDSTTGNVASFVTSFSFIIQAPNPTTTADGLAFFLAPVDTQPLDVGGMLGIFKDGYFNKSNQIVAVEFDTFSNIHFDPKGRHMGINVNSIVSIKTVPWNWTNGEVANVFISYEASTKSLTASLVYPSLETSFIVHAIVDVKDVLPEWVRFGFSATTGIDKGYVQTNDVLSWSFESNLPG 268
               SCOP domains d1fnza_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fnzA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee..........eeeeeeeee..........eeeeeeee........hhhhh....---.......eeeeee............eeeeee......eeee........eeeeeeee....eeeeeee......eeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG-------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fnz A   1 TGSLSFSFPKFAPNQPYLINQGDALVTSTGVLQLTNVVNGVPSSKSLGRALYAAPFQIWDSTTGNVASFVTSFTFIIQAPNPATTADGLAFFLAPVDTQPLDLGGMLGIFK---FNKSNQIVAVEFDTFSNGDWDPKGRHLGINVNSIESIKTVPWNWTNGEVANVFISYEASTKSLTASLVYPSLETSFIIDAIVDVKIVLPEWVRFGFSATTGIDKGYVQTNDVLSWSFESNLPG 237
                                    10        20        30        40        50        60        70        80        90       100       110|   |  120       130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                        111 115
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (LCB1_ROBPS | Q41159)
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.

 Visualization

(-) Interactive Views

Asymmetric 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
    A2G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:86 - Asp A:87   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1fnz
    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
  LCB1_ROBPS | Q41159
    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
  LCB1_ROBPS | Q41159
    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
        LCB1_ROBPS | Q41159: 1fny

(-) Related Entries Specified in the PDB File

1fny 1FNY CONTAINS BARK LECTIN.