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 :  STRUCTURE OF INVERTASE FROM SCHWANNIOMYCES OCCIDENTALIS
 
Authors :  J. Sanz-Aparicio, A. Polo
Date :  27 Oct 09  (Deposition) - 23 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Invertase, Gh32, Glycoprotein, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Alvaro-Benito, A. Polo, B. Gonzalez, M. Fernandez-Lobato, J. Sanz-Aparicio
Structural And Kinetic Analysis Of Schwanniomyces Occidentalis Invertase Reveals A New Oligomerization Patter And The Role Of Its Supplementary Domain In Substrate Binding
J. Biol. Chem. V. 285 13930 2010
PubMed-ID: 20181943  |  Reference-DOI: 10.1074/JBC.M109.095430

(-) Compounds

Molecule 1 - INVERTASE
    Chains: A, B
    EC Number: 3.2.1.26
    Organism Common: YEAST
    Organism Scientific: SCHWANNIOMYCES OCCIDENTALIS
    Organism Taxid: 27300

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:72 , ASP A:105BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWAREASN A:119 , LYS A:378BINDING SITE FOR RESIDUE NAG A 2001
03AC3SOFTWAREGLU A:200 , LYS A:202 , GLN A:204 , ASN A:219BINDING SITE FOR RESIDUE NAG A 3001
04AC4SOFTWARELEU A:306 , ASN A:334BINDING SITE FOR RESIDUE NAG A 4001
05AC5SOFTWAREASN A:394 , TYR A:478 , HOH A:645BINDING SITE FOR RESIDUE NAG A 5001
06AC6SOFTWAREASN A:49 , ASP A:50 , GLN A:68 , TRP A:76 , LEU A:80 , ASP A:179 , GLU A:230 , GOL A:6002BINDING SITE FOR RESIDUE GOL A 6001
07AC7SOFTWAREARG A:178 , GLU A:230 , ASN A:254 , TRP A:314 , GOL A:6001 , GOL A:6003BINDING SITE FOR RESIDUE GOL A 6002
08AC8SOFTWAREGOL A:6002BINDING SITE FOR RESIDUE GOL A 6003
09AC9SOFTWAREGLU B:200 , LYS B:202 , GLN B:204 , ASN B:219BINDING SITE FOR RESIDUE NAG B 3001
10BC1SOFTWAREASN B:334 , THR B:336 , HOH B:567BINDING SITE FOR RESIDUE NAG B 4001
11BC2SOFTWAREASN B:394 , TYR B:478 , HOH B:541 , HOH B:544BINDING SITE FOR RESIDUE NAG B 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KF5)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asn A:167 -Pro A:168
2Asn A:254 -Pro A:255
3Asn A:323 -Pro A:324
4Asn B:167 -Pro B:168
5Asn B:254 -Pro B:255
6Asn B:323 -Pro B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KF5)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F32PS00609 Glycosyl hydrolases family 32 active site.INV_SCHOC40-53
 		  2A:40-53
B:40-53

(-) Exons   (0, 0)

(no "Exon" information available for 3KF5)

(-) 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:512
 aligned with INV_SCHOC | P24133 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:512
                                                                                                                                                                                                                                                                                                                                                           343                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                        342  |                                                                                                                                                                                              
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333        |- |     351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531  
            INV_SCHOC    24 SIDLSVDTSEYNRPLIHFTPEKGWMNDPNGLFYDKTAKLWHLYFQYNPNATAWGQPLYWGHATSNDLVHWDEHEIAIGPEHDNEGIFSGSIVVDHNNTSGFFNSSIDPNQRIVAIYTNNIPDLQTQDIAFSLDGGYTFTKYENNPVIDVSSNQFRDPKVFWHERFKSMDHGCSEIARVKIQIFGSANLKNWVLNSNFSSGYYGNQYGMSRLIEVPIENSDKSKWVMFLAINPGSPLGGSINQYFVGDFDGFQFVPDDSQTRFVDIGKDFYAFQTFSEVEHGVLGLAWASNWQYADQVPTNPWRSSTSLARNYTLRYVIQ--MLKLTANIDKSVLPDSINVVDKLKKKNVKLTNKKPIKTNFKGSTGLFDFNITFKVLNLNVSPGKTHFDILINSQELNSSVDSIKIGFDSSQSLFYIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYGIVDKNIIELYFNDGTVAMTNTFFMGEGKYPHDIQIVTDTEEPLFELESVIIRELNK 533
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.........eeeeeeeeeeee....eeeeeeeee..........eeeeeee......ee.............eeeeeeee..................eeeeeeeee..eeeeeeeee.......ee......eeeee...eeeeeeee....eeeeeeeehhhheeeeeee......eeeeee........eeeeeeeeee......eeeeeeeee.........eeeeeeeee....eee.....ee.......eeeee.......eeeeee..............ee......eeeeeeee.......eeeeeeee......eeeeeeeeeeeee.....ee.........eeeeeeeee............eeeeee........eeeeeee....eeeee................ee..............eeeeeeee...eeeeee....eeeeee........eeeeeee.......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------GLYCOSYL_HYDRO-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kf5 A  24 SIDLSVDTSEYNRPLIHFTPEKGWMNDPNGLFYDKTAKLWHLYFQYNPNATAWGQPLYWGHATSNDLVHWDEHEIAIGPEHDNEGIFSGSIVVDHNNTSGFFNSSIDPNQRIVAIYTNNIPDNQTQDIAFSLDGGYTFTKYENNPVIDVSSNQFRDPKVFWHEDSNQWIMVVSKSQEYKIQIFGSANLKNWVLNSNFSSGYYGNQYECPGLIEVPIENSDKSKWVMFLAINPGSPLGGSINQYFVGDFDGFQFVPDDSQTRFVDIGKDFYAFQTFSEVEHGVLGLAWASNWQYADQVPTNPWRSSTSLARNYTLRYVHTNAETKQLTLIQNPVLPDSINVVDKLKKKNVKLTNKKPIKTNFKGSTGLFDFNITFKVLNLNVSPGKTHFDILINSQELNSSVDSIKIGFDSSQSSFYIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYGIVDKNIIELYFNDGTVAMTNTFFMGEGKYPHDIQIVTDTEEPLFELESVIIRELNK 535
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533  


Chain B from PDB  Type:PROTEIN  Length:508
 aligned with INV_SCHOC | P24133 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:508
                                                                                                                                                                                                                                                                                                                                                       343                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                    342  |                                                                                                                                                                                              
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    |  345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525        
            INV_SCHOC    28 SVDTSEYNRPLIHFTPEKGWMNDPNGLFYDKTAKLWHLYFQYNPNATAWGQPLYWGHATSNDLVHWDEHEIAIGPEHDNEGIFSGSIVVDHNNTSGFFNSSIDPNQRIVAIYTNNIPDLQTQDIAFSLDGGYTFTKYENNPVIDVSSNQFRDPKVFWHERFKSMDHGCSEIARVKIQIFGSANLKNWVLNSNFSSGYYGNQYGMSRLIEVPIENSDKSKWVMFLAINPGSPLGGSINQYFVGDFDGFQFVPDDSQTRFVDIGKDFYAFQTFSEVEHGVLGLAWASNWQYADQVPTNPWRSSTSLARNYTLRYVIQ--MLKLTANIDKSVLPDSINVVDKLKKKNVKLTNKKPIKTNFKGSTGLFDFNITFKVLNLNVSPGKTHFDILINSQELNSSVDSIKIGFDSSQSLFYIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYGIVDKNIIELYFNDGTVAMTNTFFMGEGKYPHDIQIVTDTEEPLFELESVIIRELNK 533
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------Glyco_hydro_32N-3kf5B01 B:40-350                                                                                                                                                                                                                                                                                       ----------------------------------------Glyco_hydro_32C-3kf5B03 B:391-493                                                                      ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Glyco_hydro_32N-3kf5B02 B:40-350                                                                                                                                                                                                                                                                                       ----------------------------------------Glyco_hydro_32C-3kf5B04 B:391-493                                                                      ------------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhh.........eeeeeeeeeeee....eeeeeeeee..........eeeeeee......ee.............eeeeeeee..................eeeeeeeee..eeeeeeeee.......ee..............eeeeeeee....eeeeeeeehhhheeeeeee......eeeeee........eeeeeeeeee......eeeeeeeee.........eeeeeeeee....eee.....ee.......eeeee.......eeeeee..............ee......eeeeeeee.......eeeeeeee......eeeeeeeeeeee......ee.........eeeeeeeee............eeeeee........eeeeeee....eeeee................ee..............eeeeeeee...eeeeee....eeeeee........eeeeeee.......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GLYCOSYL_HYDRO-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kf5 B  28 SVDTSEYNRPLIHFTPEKGWMNDPNGLFYDKTAKLWHLYFQYNPNATAWGQPLYWGHATSNDLVHWDEHEIAIGPEHDNEGIFSGSIVVDHNNTSGFFNSSIDPNQRIVAIYTNNIPDNQTQDIAFSLDGGYTFTKYENNPVIDVSSNQFRDPKVFWHEDSNQWIMVVSKSQEYKIQIFGSANLKNWVLNSNFSSGYYGNQYECPGLIEVPIENSDKSKWVMFLAINPGSPLGGSINQYFVGDFDGFQFVPDDSQTRFVDIGKDFYAFQTFSEVEHGVLGLAWASNWQYADQVPTNPWRSSTSLARNYTLRYVHTNAETKQLTLIQNPVLPDSINVVDKLKKKNVKLTNKKPIKTNFKGSTGLFDFNITFKVLNLNVSPGKTHFDILINSQELNSSVDSIKIGFDSSQSSFYIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYGIVDKNIIELYFNDGTVAMTNTFFMGEGKYPHDIQIVTDTEEPLFELESVIIRELNK 535
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527
   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 3KF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KF5)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: B_Fructosidase (34)
(-)
Clan: no clan defined [family: Glyco_hydro_32C] (13)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (INV_SCHOC | P24133)
molecular function
    GO:0004564    beta-fructofuranosidase activity    Catalysis of the reaction: a fructofuranosylated fructofuranosyl acceptor + H2O = a non fructofuranosylated fructofuranosyl acceptor + a beta-D-fructofuranoside.
    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.
    GO:0004575    sucrose alpha-glucosidase activity    Catalysis of the reaction: sucrose + H2O = alpha-D-glucose + beta-D-fructose.
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 ]
    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
    Asn A:167 - Pro A:168   [ RasMol ]  
    Asn A:254 - Pro A:255   [ RasMol ]  
    Asn A:323 - Pro A:324   [ RasMol ]  
    Asn B:167 - Pro B:168   [ RasMol ]  
    Asn B:254 - Pro B:255   [ RasMol ]  
    Asn B:323 - Pro B:324   [ 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
  3kf5
    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
  INV_SCHOC | P24133
    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)
  3.2.1.26
    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
  INV_SCHOC | P24133
    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
        INV_SCHOC | P24133: 3kf3

(-) Related Entries Specified in the PDB File

3kf3 FRUCTOFURANOSIDASE FROM SCHWANNIOMYCES OCCIDENTALIS COMPLEXED WITH FRUCTOSE