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 :  CRYSTAL STRUCTURE ANALYSIS OF SUCROSE HYDROLASE(SUH) E322Q-SUCROSE COMPLEX
 
Authors :  M. I. Kim, S. Rhee
Date :  29 Apr 08  (Deposition) - 15 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  (Alpha/Beta)8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. I. Kim, H. S. Kim, J. Jung, S. Rhee
Crystal Structures And Mutagenesis Of Sucrose Hydrolase From Xanthomonas Axonopodis Pv. Glycines: Insight Into The Exclusively Hydrolytic Amylosucrase Fold.
J. Mol. Biol. V. 380 636 2008
PubMed-ID: 18565544  |  Reference-DOI: 10.1016/J.JMB.2008.05.046
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCROSE HYDROLASE
    Chains: A
    EC Number: 3.2.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41B
    Expression System Strain: B834(DE3)PLYSS
    Expression System Vector Type: PLASMID
    Gene: SUPH
    Mutation: YES
    Organism Scientific: XANTHOMONAS AXONOPODIS PV. GLYCINES
    Organism Taxid: 92830
    Strain: 8RA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SUC1Ligand/IonSUCROSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , PHE A:140 , HIS A:180 , PHE A:244 , ARG A:278 , ASP A:280 , SER A:281 , GLN A:322 , ILE A:324 , HIS A:391 , ASP A:392 , ASP A:393 , ARG A:515 , HOH A:901 , HOH A:926 , HOH A:932 , HOH A:969BINDING SITE FOR RESIDUE SUC A 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CZK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CZK)

(-) Exons   (0, 0)

(no "Exon" information available for 3CZK)

(-) 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:618
 aligned with Q6UVM5_9XANT | Q6UVM5 from UniProtKB/TrEMBL  Length:644

    Alignment length:633
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635   
         Q6UVM5_9XANT     6 IDPPALRAAFAGPLDPQHAEVLLSRYDQHASRLLDALHALYGQRADYASWLAQWLGEVGDIARQRPQALQTLDSTRHAGWFGQPHMLGYSAYADRFAGTLQGVAERVPYLQELGVRYLHLLPFLRARAGDNDGGFAVSDYGQVEPSLGSNDDLVALTSRLREAGISLCADFVLNHTADDHAWAQAARAGDARYLDYYHHFADRTVPDRYEATLGQVFPHTAPGNFTWVDDTAQWMWTTFYPYQWDLNWSNPAVFGDMALAMLRLANLGVEAFRLDSTAYLWKRIGTDCMNQSEAHTLLVALRAVTDIVAPAVVMKAEAIVPMTQLPPYFGSGVDEGHECHLAYHSTLMAAGWSALALQRGDILHNVIAHSPPLPRHCAWLSYVRCHDDIGWNVLQHEACGNAAQPPFSLRDVARFYANAVPGSYARGESFQSSGDGVHGTNGMAAALAGIQAAQEAGDAAALAVAVDRLVLLYAIALAMPGVPLIYMGDELAMVNDPGYRDDPHRQHEGRWLHRPAMDWQLAAQRHDAKSLSGTVYRRLRGLIRQRAALGALAADQALASIALNDPRVFALTRGDSFIALHNFSDQLLDVELAAIGVDGWTLLAIDDAIGGAAARGDGSIVLPPYGVRWLQRG 638
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhh..eeee...eee..........eeeeeee.....hhhhhhhhhhhhhhh..eeeee....eee..hhhhhhhhh.hhhhhh...ee..hhhhhhhhhhh...........eeee....eeee......eee....hhhhhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhh.hhhhhhhhhh........eeeee......ee...hhhhhh........hhhhhhhhhhh.........eee.----...eee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh...hhhhhhh.....hhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...eeeeee.....eeehhhhh....ee..-----------.....eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3czk A   6 IDPPALRAAFAGPLDPQHAEVLLSRYDQHASRLLDALHALYGQRADYASWLAQWLGEVGDIARQRPQALQTLDSTRHAGWFGQPHMLGYSAYADRFAGTLQGVAERVPYLQELGVRYLHLLPFLRARAGDNDGGFAVSDYGQVEPSLGSNDDLVALTSRLREAGISLCADFVLNHTADDHAWAQAARAGDARYLDYYHHFADRTVPDRYEATLGQVFPHTAPGNFTWVDDTAQWMWTTFYPYQWDLNWSNPAVFGDMALAMLRLANLGVEAFRLDSTAYLWKRIGTDCMNQSEAHTLLVALRAVTDIVAPAVVMKAQAIVPMTQLPPYFGSGVDEGHECHLAYHSTLMAAGWSALALQRGDILHNVIAHSPPLPRHCAWLSYVRCHDDIGWNVLQHEACGNAAQPPFSLRDVARFYANAVPGSYARGESFQ----GVHGTNGMAAALAGIQAAQEAGDAAALAVAVDRLVLLYAIALAMPGVPLIYMGDELAMVNDPGYRDDPHRQHEGRWLHRPAMDWQLAAQRHDAKSLSGTVYRRLRGLIRQRAALGALAADQALASIALNDPRVFALTRGDSFIALHNFSDQLLDVELAAIGVDGWTLL-----------RGDGSIVLPPYGVRWLQRG 638
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435|    | 445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605  |      -    |  625       635   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        436  441                                                                                                                                                                    608         620
   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 3CZK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CZK)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6UVM5_9XANT | Q6UVM5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
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.

 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
    SUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3czk)
 

(-) 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
  3czk
    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
  Q6UVM5_9XANT | Q6UVM5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.48
    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
  Q6UVM5_9XANT | Q6UVM5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6UVM5_9XANT | Q6UVM5: 3cze 3czg 3czl

(-) Related Entries Specified in the PDB File

3cze THE SAME PROTEIN COMPLEXED WITH GLUCOSE
3czg
3czl