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 :  CRYSTAL STRUCTURE OF FRUCTAN 1-EXOHYDROLASE IIA FROM CICHORIUM INTYBUS
 
Authors :  M. Verhaest, W. Van Den Ende, C. J. De Ranter, A. Van Laere, A. Rabijn
Date :  25 Mar 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Five Fold Beta Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Verhaest, W. Van Den Ende, K. L. Roy, C. J. De Ranter, A. Van Laere A. Rabijns
X-Ray Diffraction Structure Of A Plant Glycosyl Hydrolase Family 32 Protein: Fructan 1-Exohydrolase Iia Of Cichorium Intybus.
Plant J. V. 41 400 2005
PubMed-ID: 15659099  |  Reference-DOI: 10.1111/J.1365-313X.2004.02304.X

(-) Compounds

Molecule 1 - FRUCTAN 1-EXOHYDROLASE IIA
    ChainsA
    EC Number3.2.1.80
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    Gene1-FEH IIA
    Organism CommonCHICORY
    Organism ScientificCICHORIUM INTYBUS
    Organism Taxid13427

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:398 , SER A:399 , ARG A:401 , GLN A:420 , ARG A:445 , ASN A:513 , NAG A:660 , HOH A:1187BINDING SITE FOR RESIDUE NDG A 650
2AC2SOFTWAREARG A:445 , NDG A:650 , MAN A:670BINDING SITE FOR RESIDUE NAG A 660
3AC3SOFTWARENAG A:660BINDING SITE FOR RESIDUE MAN A 670
4AC4SOFTWAREASN A:116 , SER A:118 , ASP A:119 , GLU A:234 , NAG A:690 , HOH A:1331BINDING SITE FOR RESIDUE NAG A 680
5AC5SOFTWARENAG A:680BINDING SITE FOR RESIDUE NAG A 690
6AC6SOFTWAREASP A:22 , SER A:83 , ARG A:146 , ASP A:147 , GLU A:201 , HOH A:1218BINDING SITE FOR RESIDUE GOL A 1758
7AC7SOFTWAREGLY A:235 , TYR A:274 , PRO A:294 , HOH A:1189 , HOH A:1252BINDING SITE FOR RESIDUE GOL A 1759
8AC8SOFTWAREPHE A:46 , TRP A:292BINDING SITE FOR RESIDUE GOL A 1760
9AC9SOFTWARELEU A:266 , ARG A:267 , TYR A:270 , GLN A:325 , PHE A:460 , ASP A:462 , LYS A:489 , THR A:490 , HOH A:1009 , HOH A:1245BINDING SITE FOR RESIDUE GOL A 1772

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:393 -A:440

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:131 -Pro A:132
2Gly A:405 -Pro A:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ST8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ST8)

(-) Exons   (0, 0)

(no "Exon" information available for 1ST8)

(-) 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:537
 aligned with Q93X60_CICIN | Q93X60 from UniProtKB/TrEMBL  Length:581

    Alignment length:537
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       
         Q93X60_CICIN    40 QIEQPYRTGYHFQPPSNWMNDPNGPMLYQGVYHFFYQYNPYAATFGDVIIWGHAVSYDLVNWIHLDPAIYPTQEADSKSCWSGSATILPGNIPAMLYTGSDSKSRQVQDLAWPKNLSDPFLREWVKHPKNPLITPPEGVKDDCFRDPSTAWLGPDGVWRIVVGGDRDNNGMAFLYQSTDFVNWKRYDQPLSSADATGTWECPDFYPVPLNSTNGLDTSVYGGSVRHVMKAGFEGHDWYTIGTYSPDRENFLPQNGLSLTGSTLDLRYDYGQFYASKSFFDDAKNRRVLWAWVPETDSQADDIEKGWAGLQSFPRALWIDRNGKQLIQWPVEEIEELRQNQVNLQNKNLKPGSVLEIHGIAASQADVTISFKLEGLKEAEVLDTTLVDPQALCNERGASSRGALGPFGLLAMASKDLKEQSAIFFRVFQNQLGRYSVLMCSDLSRSTVRSNIDTTSYGAFVDIDPRSEEISLRNLIDHSIIESFGAGGKTCITSRIYPKFVNNEEAHLFVFNNGTQNVKISEMSAWSMKNAKFVVDQS 576
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1st8A02 A:339-528 Exo-inulinase; domain 1                                                                                                                                                     ---------- CATH domains
               Pfam domains ----------Glyco_hydro_32N-1st8A01 A:12-330                                                                                                                                                                                                                                                                                               --------------------------------------Glyco_hydro_32C-1st8A02 A:369-488                                                                                       -------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee..eeeeeeeee..........eeeeeee.....eee........hhhhh.eeeeeeeeee...eeeeeeeee.....eeeeeeee..........eee.................ee.....ee.....eeeeeeeee..eeeeeeeee......ee.....eee......eeeeeeeee...............eeeeeeeee..eeeeeeeeee....eeee............ee......eeeeeeee....eeeeeeee....hhhhhhhhhee.ee...eeeee......eeeee.hhhhh.eeeeeeeeeeee...eeee.......eeeeeeeeee.hhhhhee......hhhhhhhhh..........eeeeeee.......eeeeeeeee.....eeeeeeee..............eeeee........eeeeeeee..eeeeee....eeeeee...hhhhh...eeeeee.....eeeeeeeeeee....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1st8 A   2 QIEQPYRTGYHFQPPSNWMNDPNGPMLYQGVYHFFYQYNPYAATFGDVIIWGHAVSYDLVNWIHLDPAIYPTQEADSKSCWSGSATILPGNIPAMLYTGSDSKSRQVQDLAWPKNLSDPFLREWVKHPKNPLITPPEGVKDDCFRDPSTAWLGPDGVWRIVVGGDRDNNGMAFLYQSTDFVNWKRYDQPLSSADATGTWECPDFYPVPLNSTNGLDTSVYGGSVRHVMKAGFEGHDWYTIGTYSPDRENFLPQNGLSLTGSTLDLRYDYGQFYASKSFFDDAKNRRVLWAWVPETDSQADDIEKGWAGLQSFPRALWIDRNGKQLIQWPVEEIEELRQNQVNLQNKNLKPGSVLEIHGIAASQADVTISFKLEGLKEAEVLDTTLVDPQALCNERGASSRGALGPFGLLAMASKDLKEQSAIFFRVFQNQLGRYSVLMCSDLSRSTVRSNIDTTSYGAFVDIDPRSEEISLRNLIDHSIIESFGAGGKTCITSRIYPKFVNNEEAHLFVFNNGTQNVKISEMSAWSMKNAKFVVDQS 538
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       

   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  (0, 0)

(no "SCOP Domain" information available for 1ST8)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q93X60_CICIN | Q93X60)
molecular function
    GO:0051669    fructan beta-fructosidase activity    Catalysis of the hydrolysis of terminal, non-reducing 2,1- and 2,6-linked beta-D-fructofuranose residues in fructans.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDG  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:131 - Pro A:132   [ RasMol ]  
    Gly A:405 - Pro A:406   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1st8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q93X60_CICIN | Q93X60
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.80
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q93X60_CICIN | Q93X60
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q93X60_CICIN | Q93X602add 2ade 2aey 2aez

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ST8)