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 OF 2-DEOXY-SCYLLO-INOSOSE SYNTHASE
 
Authors :  E. Nango, T. Kumasaka, N. Tanaka, K. Kakinuma, T. Eguchi
Date :  20 Sep 05  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, 2-Deoxystreptamine, Dehydroquinate Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Nango, T. Kumasaka, T. Hirayama, N. Tanaka, T. Eguchi
Structure Of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme In The Biosynthesis Of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, In Complex With A Mechanism-Based Inhibitor And Nad+
Proteins V. 70 517 2008
PubMed-ID: 17879343  |  Reference-DOI: 10.1002/PROT.21526

(-) Compounds

Molecule 1 - 2-DEOXY-SCYLLO-INOSOSE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2GOL3Ligand/IonGLYCEROL
3SO32Ligand/IonSULFITE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:183 , HIS A:246 , HIS A:262 , HOH A:773 , HOH A:774 , HOH A:801BINDING SITE FOR RESIDUE CO A 601
2AC2SOFTWAREASP A:42 , GLY A:103 , LEU A:105 , THR A:106BINDING SITE FOR RESIDUE CO A 603
3AC3SOFTWAREGLU A:235 , GLY A:239 , GLU A:243 , HOH A:630 , HOH A:631BINDING SITE FOR RESIDUE CO A 604
4AC4SOFTWAREGLU A:243 , TYR A:244 , GLY A:245 , HIS A:246 , THR A:247 , ALA A:273 , MET A:335 , ILE A:336 , HOH A:628BINDING SITE FOR RESIDUE SO3 A 608
5AC5SOFTWAREGLU B:183 , HIS B:246 , HIS B:262 , GOL B:606 , HOH B:788BINDING SITE FOR RESIDUE CO B 602
6AC6SOFTWAREGLU B:243 , TYR B:244 , GLY B:245 , HIS B:246 , THR B:247 , ALA B:273 , MET B:335 , ILE B:336 , HOH B:626BINDING SITE FOR RESIDUE SO3 B 609
7AC7SOFTWAREGLY A:104 , THR A:129 , LEU A:131 , HOH A:610 , HOH A:635BINDING SITE FOR RESIDUE GOL A 607
8AC8SOFTWAREGLY B:104 , THR B:129 , LEU B:131 , HOH B:617 , HOH B:649BINDING SITE FOR RESIDUE GOL B 605
9AC9SOFTWAREASP B:135 , GLU B:183 , HIS B:246 , HIS B:262 , CO B:602 , HOH B:686BINDING SITE FOR RESIDUE GOL B 606

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:12
2B:7 -B:12

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D2X)

(-) Exons   (0, 0)

(no "Exon" information available for 2D2X)

(-) 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:353
 aligned with DOIS_BACCI | Q9S5E2 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:367
                                    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       
           DOIS_BACCI     2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee..hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhh----...hhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhh----------..eeee..eee..ee........eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2x A   2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLIL----KEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIH----------EDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
                                    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       | -       331       341       351       361       
                                                                                                                                                                                                                       191  196                                                                                                                        319        330                                      


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with DOIS_BACCI | Q9S5E2 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:367
                                    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       
           DOIS_BACCI     2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee..hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh.eeeeee..eeeeeeee....eeeeehhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......----hhhhhhhhhh-----------..eeeee.eee..ee.......eeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2x B   2 TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVHYAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAVGGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKNLVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTEDDLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDI----DPDSIFHYLI-----------EDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIREGL 368
                                    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      |  -       331       341       351       361       
                                                                                                                                                                                                                                                                                                                                        304  309      318         330
   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 2D2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D2X)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DOIS_BACCI | Q9S5E2)
molecular function
    GO:0016838    carbon-oxygen lyase activity, acting on phosphates    Catalysis of the cleavage of a carbon-oxygen bond by elimination of a phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).

 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
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO3  [ 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
(no "Cis Peptide Bonds" information available for 2d2x)
 

(-) 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
  2d2x
    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
  DOIS_BACCI | Q9S5E2
    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)
  4.2.3.-
    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
  DOIS_BACCI | Q9S5E2
    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
        DOIS_BACCI | Q9S5E2: 2gru

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2D2X)