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 :  FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 9 MIN OF SOAKING
 
Authors :  M. Veelders, L. -O. Essen
Date :  07 Feb 12  (Deposition) - 03 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Adhesin, Flocculin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Veelders, L. -O. Essen
Complex Gadolinium-Oxo Clusters Formed Along Concave Protein Surfaces.
Chembiochem V. 13 2187 2012
PubMed-ID: 22936626  |  Reference-DOI: 10.1002/CBIC.201200441

(-) Compounds

Molecule 1 - FLOCCULATION PROTEIN FLO5
    Atcc: 204508
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: ORIGAMI 2
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: LECTIN-LIKE DOMAIN, RESIDUES 23-271
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Other Details: SOAKED 9 MIN WITH GDAC3
    Strain: S288C
    Synonym: FLOCCULIN-5, FLO5A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GD11Ligand/IonGADOLINIUM ATOM

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:160 , ASP A:161 , ASN A:224 , VAL A:226 , TRP A:228 , HOH A:2219 , HOH A:2221 , HOH A:2266BINDING SITE FOR RESIDUE GD A1272
02AC2SOFTWAREASP A:78 , ASP A:245 , GD A:1277 , HOH A:2114 , HOH A:2116 , HOH A:2117 , HOH A:2126BINDING SITE FOR RESIDUE GD A1273
03AC3SOFTWAREASP A:82 , ASP A:125 , GD A:1275 , GD A:1276 , GD A:1279 , HOH A:2123 , HOH A:2124 , HOH A:2127BINDING SITE FOR RESIDUE GD A1274
04AC4SOFTWAREASP A:125 , GD A:1274 , GD A:1276 , HOH A:2127 , HOH A:2188 , HOH A:2189 , HOH A:2308BINDING SITE FOR RESIDUE GD A1275
05AC5SOFTWAREGD A:1274 , GD A:1275 , HOH A:2116 , HOH A:2126 , HOH A:2127 , HOH A:2128 , HOH A:2308BINDING SITE FOR RESIDUE GD A1276
06AC6SOFTWAREGD A:1273 , HOH A:2117 , HOH A:2128BINDING SITE FOR RESIDUE GD A1277
07AC7SOFTWAREASP A:78 , HOH A:2116 , HOH A:2117BINDING SITE FOR RESIDUE GD A1278
08AC8SOFTWAREASP A:125 , GD A:1274 , HOH A:2124 , HOH A:2128 , HOH A:2190BINDING SITE FOR RESIDUE GD A1279
09AC9SOFTWAREGLU A:236 , HOH A:2267 , HOH A:2269BINDING SITE FOR RESIDUE GD A1280
10BC1SOFTWAREGLU A:179 , HOH A:2233 , HOH A:2235 , HOH A:2309BINDING SITE FOR RESIDUE GD A1281
11BC2SOFTWARESER A:170 , GLU A:174 , HOH A:2023BINDING SITE FOR RESIDUE GD A1282
12BC3SOFTWARETYR A:102 , CYS A:107 , GLY A:109 , GLY A:111BINDING SITE FOR RESIDUE CL A1283
13BC4SOFTWAREPHE A:94 , PRO A:95 , HOH A:2135BINDING SITE FOR RESIDUE CL A1284

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:29 -A:175
2A:87 -A:113
3A:96 -A:107
4A:176 -A:263

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:104 -Trp A:105
2Asp A:160 -Asp A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AI0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA14PS51820 PA14 domain profile.FLO5_YEAST74-249  1A:74-249

(-) Exons   (0, 0)

(no "Exon" information available for 4AI0)

(-) 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:258
 aligned with FLO5_YEAST | P38894 from UniProtKB/Swiss-Prot  Length:1075

    Alignment length:258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263        
           FLO5_YEAST    14 AFLALINVASGATEACLPAGQRKSGMNINFYQYSLKDSSTYSNAAYMAYGYASKTKLGSVGGQTDISIDYNIPCVSSSGTFPCPQEDSYGNWGCKGMGACSNSQGIAYWSTDLFGFYTTPTNVTLEMTGYFLPPQTGSYTFSFATVDDSAILSVGGSIAFECCAQEQPPITSTNFTINGIKPWDGSLPDNITGTVYMYAGYYYPLKVVYSNAVSWGTLPISVELPDGTTVSDNFEGYVYSFDDDLSQSNCTIPDPSIH 271
               SCOP domains d4ai0a_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh...ee......ee.eeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee....eee..eeee..eeee.hhh.ee...ee...ee.......................eeeeeeeee.....eeeeeee.....eeeeee......................eee...........eeeeeee.....eeeeeeeee....eee.eeee.....eee......eee..........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PA14  PDB: A:74-249 UniProt: 74-249                                                                                                                                             ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ai0 A  14 GLVPRGSHMSGATEACLPAGQRKSGMNINFYQYSLKDSSTYSNAAYMAYGYASKTKLGSVGGQTDISIDYNIPCVSSSGTFPCPQEDSYGNWGCKGMGACSNSQGIAYWSTDLFGFYTTPTNVTLEMTGYFLPPQTGSYTFSFATVDDSAILSVGGSIAFECCAQEQPPITSTNFTINGIKPWDGSLPDNITGTVYMYAGYYYPLKVVYSNAVSWGTLPISVELPDGTTVSDNFEGYVYSFDDDLSQSNCTIPDPSIH 271
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AI0)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FLO5_YEAST | P38894)
molecular function
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
biological process
    GO:0031589    cell-substrate adhesion    The attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0036281    coflocculation    The non-sexual aggregation between single-celled organisms of different species.
    GO:0000128    flocculation    The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs.
    GO:0000501    flocculation via cell wall protein-carbohydrate interaction    The reversible, non-sexual aggregation of cells mediated by the binding of proteins in the cell wall of one cell to carbohydrates in the cell wall of another cell. An example of this process is found in Saccharomyces cerevisiae, in which it is pH- and calcium-dependent.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0009277    fungal-type cell wall    A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GD  [ 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 ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:104 - Trp A:105   [ RasMol ]  
    Asp A:160 - Asp A:161   [ 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
  4ai0
    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
  FLO5_YEAST | P38894
    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
  FLO5_YEAST | P38894
    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
        FLO5_YEAST | P38894: 2xjp 2xjq 2xjr 2xjs 2xjt 2xju 2xjv 4ahw 4ahx 4ahy 4ahz 4ai1 4ai2 4ai3

(-) Related Entries Specified in the PDB File

2xjp X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH CALCIUM AND MANNOSE
2xjq X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE
2xjr X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH CALCIUM AND MAN5(D2-D3)
2xjs X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH CALCIUM AND A1,2-MANNOBIOSE
2xjt X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH CALCIUM AND MAN5(D1)
2xju X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE WITH MUTATION S227A IN COMPLEX WITH CALCIUM AND A1,2-MANNOBIOSE
2xjv X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF THE FLOCCULIN FLO5 FROM SACCHAROMYCES CEREVISIAE WITH MUTATION D201T IN COMPLEX WITH CALCIUM AND GLUCOSE
4ahw FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE
4ahx FLO5A SHOWING A TRINUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE
4ahy FLO5A COCRYSTALLIZED WITH 3 MM GDAC3
4ahz FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 60 MIN OF SOAKING
4ai1 FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 19 MIN OF SOAKING
4ai2 FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 41 MIN OF SOAKING
4ai3 FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 60 MIN OF SOAKING