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 CELLVIBRIO CELLULOSA ALPHA-L-ARABINANASE COMPLEXED WITH ARABINOHEXAOSE
 
Authors :  D. Nurizzo, J. P. Turkenburg, S. J. Charnock, S. M. Roberts, E. J. Dodson V. A. Mckie, E. J. Taylor, H. J. Gilbert, G. J. Davies
Date :  23 Apr 02  (Deposition) - 23 Aug 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  B
Keywords :  Arabinanase, Hydrolase, Propeller, Catalysis, Cellvibrio, Pseudomonas (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nurizzo, J. P. Turkenburg, S. J. Charnock, S. M. Roberts, E. J. Dodson, V. A. Mckie, E. J. Taylor, H. J. Gilbert, G. J. Davies
Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has A Novel Five-Blade Beta-Propeller Fold
Nat. Struct. Biol. V. 9 665 2002
PubMed-ID: 12198486  |  Reference-DOI: 10.1038/NSB835

(-) Compounds

Molecule 1 - ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
    Chains: B
    EC Number: 3.2.1.99
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(PLYSS)
    Expression System Plasmid: PVM1
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: CELLVIBRIO CELLULOSA
    Organism Taxid: 155077
    Synonym: ALPHA-L-ARABINANASE, ABN A, ENDO-1,5-ALPHA-L-ARABINANASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1AHR6Ligand/IonALPHA-L-ARABINOFURANOSE
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:114 , GLY B:115 , LYS B:116 , AHR B:802BINDING SITE FOR RESIDUE AHR B 801
2AC2SOFTWAREGLY B:115 , AHR B:801 , AHR B:803BINDING SITE FOR RESIDUE AHR B 802
3AC3SOFTWAREALA B:113 , PHE B:114 , GLY B:115 , ASN B:155 , SER B:175 , PHE B:176 , AHR B:802 , AHR B:804 , HOH B:2076BINDING SITE FOR RESIDUE AHR B 803
4AC4SOFTWAREASP B:38 , TRP B:94 , GLU B:221 , CYS B:241 , AHR B:803 , AHR B:805BINDING SITE FOR RESIDUE AHR B 804
5AC5SOFTWARETRP B:94 , AHR B:804 , AHR B:806BINDING SITE FOR RESIDUE AHR B 805
6AC6SOFTWAREASP B:35 , VAL B:36 , THR B:53 , GLY B:54 , HIS B:92 , GLN B:316 , AHR B:805BINDING SITE FOR RESIDUE AHR B 806
7AC7SOFTWAREHIS B:291 , HOH B:2009 , HOH B:2024 , HOH B:2025 , HOH B:2049 , HOH B:2070 , HOH B:2071BINDING SITE FOR RESIDUE CL B 901

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:241 -B:242

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu B:194 -Pro B:195
2Gly B:261 -Pro B:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GYE)

(-) 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 B from PDB  Type:PROTEIN  Length:315
 aligned with ARBA_CELJU | P95470 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:315
                                    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     
           ARBA_CELJU    32 KQVDVHDPVMTREGDTWYLFSTGPGITIYSSKDRVNWRYSDRAFGTEPTWAKRVSPSFDGHLWAPDIYQHKGLFYLYYSVSAFGKNTSAIGVTVNKTLNPASPDYRWEDKGIVIESVPQRDLWNAIDPAIIADDHGQVWMSFGSFWGGLKLFKLNDDLTRPAEPQEWHSIAKLERSVLMDDSQAGSAQIEAPFILRKGDYYYLFASWGLCCRKGDSTYHLVVGRSKQVTGPYLDKTGRDMNQGGGSLLIKGNKRWVGLGHNSAYTWDGKDYLVLHAYEAADNYLQKLKILNLHWDGEGWPQVDEKELDSYISQRL 346
               SCOP domains d1gyeb_ B: alpha-L-arabinanase                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gyeB00 B:32-346 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eeeeee.ee..eeeee....eeeeeee.......hhhhhh.....eeeeeeeeee..eeeeeeee.......eeeeeeee............eeeeeeeee............eeee.....eeeee......eeeee.............eeeee.................eeeeeeeee..eeeeeeee....hhhhh..eeeeeee..............hhhh..eeee.....eeeeeeeeeeee..eeeeeeeeee.hhh..eeeeeee.ee.....ee...hhhhhh..eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gye B  32 KQVDVHDPVMTREGATWYLFSTGPGITIYSSKDRVNWRYSDRAFATEPTWAKRVSPSFDGHLWAPDIYQHKGLFYLYYSVSAFGKNTSAIGVTVNKTLNPASPDYRWEDKGIVIESVPQRDLWNAIAPAIIADDHGQVWMSFGSFWGGLKLFKLNDDLTRPAEPQEWHSIAKLERSVLMDDSQAGSAQIEAPFILRKGDYYYLFASWGLCCRKGDSTYHLVVGRSKQVTGPYLDKTGRDMNQGGGSLLIKGNKRWVGLGHNSAYTWDGKDYLVLHAYEAADNYLQKLKILNLHWDGEGWPQVDEKELDSYISQRL 346
                                    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
   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (ARBA_CELJU | P95470)
molecular function
    GO:0046558    arabinan endo-1,5-alpha-L-arabinosidase activity    Catalysis of the endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5) arabinans.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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: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.

 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
    AHR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ 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 ]
 
  Cis Peptide Bonds
    Glu B:194 - Pro B:195   [ RasMol ]  
    Gly B:261 - Pro B:262   [ 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
  1gye
    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
  ARBA_CELJU | P95470
    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)
  3.2.1.99
    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
  ARBA_CELJU | P95470
    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
        ARBA_CELJU | P95470: 1gyd 1gyh

(-) Related Entries Specified in the PDB File

1gyd STRUCTURE OF CELLVIBRIO CELLULOSA ALPHA-L- ARABINANASE
1gyh STRUCTURE OF D158A CELLVIBRIO CELLULOSA ALPHA -L-ARABINANASE MUTANT