Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - 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 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 :  X-RAY CRYSTAL STRUCTURE OF XEROCOMUS CHRYSENTERON LECTIN XCL AT 1.4 ANGSTROMS RESOLUTION, MUTATED AT Q46M, V54M, L58M
 
Authors :  C. Birck, L. Damian, C. Marty-Detraves, A. Lougarre, C. Schulze-Bries P. Koehl, D. Fournier, L. Paquereau, J. P. Samama
Date :  20 Aug 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Fungal Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Birck, L. Damian, C. Marty-Detraves, A. Lougarre, C. Schulze-Briese, P. Koehl, D. Fournier, L. Paquereau, J. P. Samama
A New Lectin Family With Structure Similarity To Actinoporins Revealed By The Crystal Structure Of Xerocomus Chrysenteron Lectin Xcl
J. Mol. Biol. V. 344 1409 2004
PubMed-ID: 15561152  |  Reference-DOI: 10.1016/J.JMB.2004.10.007

(-) Compounds

Molecule 1 - LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: XEROCOMUS CHRYSENTERON
    Organism Taxid: 5386
    Synonym: XCL LECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3SO410Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:2 , MSE A:3 , TYR A:76 , HOH A:923 , HOH A:936BINDING SITE FOR RESIDUE SO4 A 900
2AC2SOFTWAREARG A:66 , LYS B:77 , ARG B:78BINDING SITE FOR RESIDUE SO4 B 901
3AC3SOFTWARELYS A:77 , ARG A:78BINDING SITE FOR RESIDUE SO4 A 902
4AC4SOFTWAREHIS A:74 , ARG A:109 , GLU A:110 , HOH A:932 , HOH A:977BINDING SITE FOR RESIDUE SO4 A 903
5AC5SOFTWAREGLY B:19 , THR B:62 , LYS B:63BINDING SITE FOR RESIDUE SO4 B 904
6AC6SOFTWARESER A:4 , TYR A:5 , SER A:6 , ASN A:102 , ASN A:136 , EDO A:802 , HOH A:937 , HOH A:979BINDING SITE FOR RESIDUE EDO A 801
7AC7SOFTWAREASN A:102 , ASP A:106 , GLU A:110 , EDO A:801 , HOH A:932 , HOH A:979BINDING SITE FOR RESIDUE EDO A 802
8AC8SOFTWARESER A:51 , GLY A:52 , ASN A:75 , HOH A:931 , HOH A:964BINDING SITE FOR RESIDUE EDO A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X99)

(-) Exons   (0, 0)

(no "Exon" information available for 1X99)

(-) 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:145
 aligned with Q8WZC9_9HOMO | Q8WZC9 from UniProtKB/TrEMBL  Length:143

    Alignment length:145
                              1                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138     
         Q8WZC9_9HOMO     - --MSYSITLRVYQTNRDRGYFSIVEKTVWHFANGGTWSEANGAHTLTQGGSGTSGVLRFLSTKGERITVAVGVHNYKRWCDVVTGLKPDETALVINPQYYNNGGRDYVREKQLAEYSVTSAIGTKVEVVYTVAEGNNLEANVIFS 143
               SCOP domains d1x99a_ A: Lectin xcl                                                                                                                             SCOP domains
               CATH domains 1x99A00 A:1-145  [code=2.60.270.20, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhh.eeeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeee..eeeeeee.......hhhhhhhhhh....hhhhhhh...eeeee.....eeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x99 A   1 GHmSYSITLRVYQTNRDRGYFSIVEKTVWHFANGGTWSEANGAHTLTmGGSGTSGmLRFmSTKGERITVAVGVHNYKRWCDVVTGLKPDETALVINPQYYNNGGRDYVREKQLAEYSVTSAIGTKVEVVYTVAEGNNLEANVIFS 145
                              |     10        20        30        40       |50     |  60        70        80        90       100       110       120       130       140     
                              |                                           48-MSE  56-MSE                                                                                     
                              3-MSE                                                   60-MSE                                                                                 


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with Q8WZC9_9HOMO | Q8WZC9 from UniProtKB/TrEMBL  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
         Q8WZC9_9HOMO     1 MSYSITLRVYQTNRDRGYFSIVEKTVWHFANGGTWSEANGAHTLTQGGSGTSGVLRFLSTKGERITVAVGVHNYKRWCDVVTGLKPDETALVINPQYYNNGGRDYVREKQLAEYSVTSAIGTKVEVVYTVAEGNNLEANVIFS 143
               SCOP domains d1x99b_ B: Lectin xcl                                                                                                                           SCOP domains
               CATH domains -1x99B00 B:4-145  [code=2.60.270.20, no name defined]                                                                                           CATH domains
           Pfam domains (1) FB_lectin-1x99B01 B:3-143                                                                                                                    -- Pfam domains (1)
           Pfam domains (2) FB_lectin-1x99B02 B:3-143                                                                                                                    -- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.......eeeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeee..eeeeeee.......hhhhhhhhhh....hhhhhhh...eeeee.....eeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x99 B   3 mSYSITLRVYQTNRDRGYFSIVEKTVWHFANGGTWSEANGAHTLTmGGSGTSGmLRFmSTKGERITVAVGVHNYKRWCDVVTGLKPDETALVINPQYYNNGGRDYVREKQLAEYSVTSAIGTKVEVVYTVAEGNNLEANVIFS 145
                            |       12        22        32        42     |  52   |   |62        72        82        92       102       112       122       132       142   
                            3-MSE                                       48-MSE  56-MSE                                                                                     
                                                                                    60-MSE
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: FB_lectin] (4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1X99)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
(no "Cis Peptide Bonds" information available for 1x99)
 
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
  1x99
    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
  Q8WZC9_9HOMO | Q8WZC9
    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
  Q8WZC9_9HOMO | Q8WZC9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8WZC9_9HOMO | Q8WZC9: 1xi0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X99)