Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  CRYSTAL STRUCTURE OF A FAMILY 51 (GH51) ALPHA-L-ARABINOFURANOSIDASE FROM GEOBACILLUS STEAROTHERMOPHILUS T6
 
Authors :  K. Hoevel, D. Shallom, K. Niefind, V. Belakhov, G. Shoham, T. Baasov, Y. D. Schomburg
Date :  09 Jul 03  (Deposition) - 07 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Beta-Alpha8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hoevel, D. Shallom, K. Niefind, V. Belakhov, G. Shoham, T. Baasov, Y. Shoham, D. Schomburg
Crystal Structure And Snapshots Along The Reaction Pathway Of A Family 51 Alpha-L-Arabinofuranosidase
Embo J. V. 22 4922 2003
PubMed-ID: 14517232  |  Reference-DOI: 10.1093/EMBOJ/CDG494

(-) Compounds

Molecule 1 - ALPHA-L-ARABINOFURANOSIDASE
    Chains: A, B
    EC Number: 3.2.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ABFA
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: T-6
    Synonym: ARABINOSIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:27 , TRP A:99 , TYR A:246 , GLU A:294 , TRP A:298 , GLN A:351 , HOH A:546 , HOH A:793 , HOH A:851 , HOH A:854BINDING SITE FOR RESIDUE GOL A 503
2AC2SOFTWAREPHE B:27 , ASN B:74 , TRP B:99 , TYR B:246 , GLU B:294 , TRP B:298 , GLN B:351 , HOH B:505 , HOH B:959BINDING SITE FOR RESIDUE GOL B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PZ3)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:70 -Pro A:71
2Gly A:72 -Gly A:73
3Ala A:350 -Gln A:351
4Tyr B:70 -Pro B:71
5Gly B:72 -Gly B:73
6Ala B:350 -Gln B:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 1PZ3)

(-) 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:497
 aligned with IABF_GEOSE | Q9XBQ3 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:497
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       
           IABF_GEOSE     5 KATMIIEKDFKIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPIIRYPGGNFVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNLGTRGIDAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNEMDGPWQIGHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPTFAEWEATVLDHTYDHVDYISLHQYYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSFDEWNVWYHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIACLAQLVNVIAPIMTEKNGPAWKQTIYYPFMHASVYGRGVALHPVISSPKYDSKDFTDVPYLESIAVYNEEKEEVTIFAVNRDMEDALLLECDVRSFEDYRVIEHIVLEHDNVKQTNSAQSSPVVPHRNGDAQLSDRKVSATLPKLSWNVIRLGK 501
               SCOP domains d1pz3a1      d1pz3a2 A:18-384 Alpha-L-arabinofuranosidase, catalytic domain                                                                                                                                                                                                                                                                                                                 d1pz3a1 A:5-17,A:385-501 Alpha-l-arabinofuranosidase                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee.hhhhheee.........................hhhhhhhhhhhh..eeee..hhhhhhhhhhhhh.hhhhh..eee....eee....hhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhh...hhhhhhhhhh.........eeee.............hhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhh................hhhhhhhhhhhhhhhhhh...eeeeeee........eee.....eee..hhhhhhhhhhhh..eee..eee..ee.......ee.eeeeeeee....eeeeeeee......eeeeee.......eeeeeeee........................eee..eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pz3 A   5 KATMIIEKDFKIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPIIRYPGGNFVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNLGTRGIDAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNEMDGPWQIGHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPTFAEWEATVLDHTYDHVDYISLHQYYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSFDEWNVWYHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIACLAQLVNVIAPIMTEKNGPAWKQTIYYPFMHASVYGRGVALHPVISSPKYDSKDFTDVPYLESIAVYNEEKEEVTIFAVNRDMEDALLLECDVRSFEDYRVIEHIVLEHDNVKQTNSAQSSPVVPHRNGDAQLSDRKVSATLPKLSWNVIRLGK 501
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with IABF_GEOSE | Q9XBQ3 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:497
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       
           IABF_GEOSE     5 KATMIIEKDFKIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPIIRYPGGNFVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNLGTRGIDAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNEMDGPWQIGHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPTFAEWEATVLDHTYDHVDYISLHQYYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSFDEWNVWYHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIACLAQLVNVIAPIMTEKNGPAWKQTIYYPFMHASVYGRGVALHPVISSPKYDSKDFTDVPYLESIAVYNEEKEEVTIFAVNRDMEDALLLECDVRSFEDYRVIEHIVLEHDNVKQTNSAQSSPVVPHRNGDAQLSDRKVSATLPKLSWNVIRLGK 501
               SCOP domains d1pz3b1      d1pz3b2 B:18-384 Alpha-L-arabinofuranosidase, catalytic domain                                                                                                                                                                                                                                                                                                                 d1pz3b1 B:5-17,B:385-501 Alpha-l-arabinofuranosidase                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee.hhhhheee.........................hhhhhhhhhhhh..eeee..hhhhhhhhhhhhh.hhhhh..eee....eee....hhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhh...hhhhhhhhhh.........eeee.............hhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhh................hhhhhhhhhhhhhhhhhh...eeeeeee........eee.....eee..hhhhhhhhhhhh..eee..eee..ee.......ee.eeeeeeee....eeeeeeee......eeeeee.......eeeeeeeee.......................eee..eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pz3 B   5 KATMIIEKDFKIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPIIRYPGGNFVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNLGTRGIDAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNEMDGPWQIGHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPTFAEWEATVLDHTYDHVDYISLHQYYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSFDEWNVWYHSNEADKLIEPWTVAPPLLEDIYNFEDALLVGCMLITLMKHADRVKIACLAQLVNVIAPIMTEKNGPAWKQTIYYPFMHASVYGRGVALHPVISSPKYDSKDFTDVPYLESIAVYNEEKEEVTIFAVNRDMEDALLLECDVRSFEDYRVIEHIVLEHDNVKQTNSAQSSPVVPHRNGDAQLSDRKVSATLPKLSWNVIRLGK 501
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PZ3)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IABF_GEOSE | Q9XBQ3)
molecular function
    GO:0046556    alpha-L-arabinofuranosidase activity    Catalysis of the hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
    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.
biological process
    GO:0046373    L-arabinose metabolic process    The chemical reactions and pathways involving L-arabinose, the D-enantiomer of arabino-pentose. L-arabinose occurs free, e.g. in the heartwood of many conifers, and in the combined state, in both furanose and pyranose forms, as a constituent of various plant hemicelluloses, bacterial polysaccharides etc.
    GO:0031222    arabinan catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinan, a polysaccharide composed of arabinose residues.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:350 - Gln A:351   [ RasMol ]  
    Ala B:350 - Gln B:351   [ RasMol ]  
    Gly A:72 - Gly A:73   [ RasMol ]  
    Gly B:72 - Gly B:73   [ RasMol ]  
    Tyr A:70 - Pro A:71   [ RasMol ]  
    Tyr B:70 - Pro B:71   [ 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
  1pz3
    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
  IABF_GEOSE | Q9XBQ3
    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)
  3.2.1.55
    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
  IABF_GEOSE | Q9XBQ3
    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
        IABF_GEOSE | Q9XBQ3: 1pz2 1qw8 1qw9

(-) Related Entries Specified in the PDB File

1pz2 CRYSTAL STRUCTURE OF A TRANSIENT COVALENT REACTION INTERMEDIATE OF A FAMILY 51 ALPHA-L-ARABINOFURANOSIDASE
1qw8 CRYSTAL STRUCTURE OF A FAMILY 51 ALPHA-L- ARABINOFURANOSIDASE IN COMPLEX WITH ARA-ALPHA(1,3)-XYL
1qw9 CRYSTAL STRUCTURE OF A FAMILY 51 ALPHA-L- ARABINOFURANOSIDASE IN COMPLEX WITH 4-NITROPHENYL-ARA