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 THE PREALNUMYCIN C-GLYCOSYNTHASE ALNA IN COMPLEX WITH RIBULOSE 5-PHOSPHATE
 
Authors :  T. Oja, L. Niiranen, T. Sandalova, Klika K. D. , J. Niemi, P. Mantsala, G. Schneider, M. Metsa-Ketela
Date :  30 Apr 12  (Deposition) - 16 Jan 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Alpha/Beta/Alpha-Domain, C-Glycosynthase, Ribose 5-Phosphate Binding, Divalent Metal Ion Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Oja, L. Niiranen, T. Sandalova, K. D. Klika, J. Niemi, P. Mantsala, G. Schneider, M. Metsa-Ketela
Structural Basis For C-Ribosylation In The Alnumycin A Biosynthetic Pathway.
Proc. Natl. Acad. Sci. Usa V. 110 1291 2013
PubMed-ID: 23297194  |  Reference-DOI: 10.1073/PNAS.1207407110

(-) Compounds

Molecule 1 - ALNA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBADDELHISB
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALNA
    Organism Scientific: STREPTOMYCES SP. CM020
    Organism Taxid: 569580
    Strain: SP. CM020

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
15RP1Ligand/IonRIBULOSE-5-PHOSPHATE
2CA2Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
15RP3Ligand/IonRIBULOSE-5-PHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:138 , GLU A:169 , GLU A:172 , ASN A:259 , HOH A:501BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:29 , THR A:105 , VAL A:106 , HIS A:130 , SER A:140 , PRO A:141 , ASP A:142 , LYS A:159 , HOH A:502BINDING SITE FOR RESIDUE 5RP A 402
3AC3SOFTWAREASP A:135BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREARG A:147BINDING SITE FOR RESIDUE EPE A 404
5AC5SOFTWARELYS A:86BINDING SITE FOR RESIDUE CL A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EX9)

(-) Exons   (0, 0)

(no "Exon" information available for 4EX9)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee..eeee..hhhhhhhhhhh....eehhhhhhhhhhhh.eeeehhhhhhhhhhhhh..eee.........hhhhhh...hhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee...eeee..eeeeeee.eee.hhhhhhhhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ex9 A   5 PDQLLEVSDEIATALAERRPVVALESSLITTDPSSETASLIEKAVRGAGAVPATIGIAGGKLVVGLTDSLIERFASTKGIPKISARDIGGALAGGGLGATTVAGTIVIAERAGIQVFTTAGIGGVHRRGEDTLDISPDLLQFRKTKMTVVSGGAKSILDHRLTAEYLETAGVPVYGYRTDKLAAFVVREADVPVTRMDDLHTAARAAEAHWQVNGPGTVLLTSPIDEQDAVDEAIVEAAIAEALAQCDQEGIVGNAVSPYLMKALARASGGMLPKAGRSLLLSTARVAGEFSAALSAVQAER 306
                                    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
   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 4EX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EX9)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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
    5RP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ex9)
 
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
  4ex9
    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
  B6SEG5_9ACTN | B6SEG5
    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)
  (no 'Enzyme Classificator' available)
    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
  B6SEG5_9ACTN | B6SEG5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B6SEG5_9ACTN | B6SEG5: 4ex8

(-) Related Entries Specified in the PDB File

4ex6 4ex7 4ex8