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 A.FULGIDUS RIO2 KINASE COMPLEXED WITH ADP AND MANGANESE IONS
 
Authors :  N. Laronde-Leblanc, T. Guszczynski, T. Copeland, A. Wlodawer
Date :  06 Apr 05  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Kinase, Winged-Helix, Rio Domain, Adp-Mn Complex, Rrna Processing, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Laronde-Leblanc, T. Guszczynski, T. Copeland, A. Wlodawer
Autophosphorylation Of Archaeoglobus Fulgidus Rio2 And Crystal Structures Of Its Nucleotide-Metal Ion Complexes.
Febs J. V. 272 2800 2005
PubMed-ID: 15943813  |  Reference-DOI: 10.1111/J.1742-4658.2005.04702.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIO2 KINASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: ROSETTA-PLYSS-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIO2
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:223 , ASP A:235 , ADP A:401 , HOH A:423 , HOH A:489BINDING SITE FOR RESIDUE MN A 402
2AC2SOFTWAREGLU A:103 , SER A:104 , VAL A:118 , LYS A:120 , MET A:179 , GLU A:180 , ILE A:182 , GLU A:186 , TYR A:222 , ASN A:223 , ILE A:234 , ASP A:235 , MN A:402 , HOH A:423 , HOH A:477 , HOH A:478 , HOH A:564BINDING SITE FOR RESIDUE ADP A 401
3AC3SOFTWAREASN A:153 , ALA A:157 , LYS A:160 , SER A:239 , GLU A:241BINDING SITE FOR RESIDUE EDO A 403
4AC4SOFTWAREGLN A:162 , GLY A:163 , LEU A:164 , VAL A:166 , LYS A:168BINDING SITE FOR RESIDUE EDO A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZAR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZAR)

(-) 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:267
 aligned with RIO2_ARCFU | O30245 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:280
                                    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
           RIO2_ARCFU     2 NIAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNRQKDYEGSTFTFIGLSLYSLHRLVRSGKVDAIGKLMGEGKESAVFNCYSEKFGECVVKFHKVGHTSFKKVKEKRDYGDLHFSVLAIRSARNEFRALQKLQGLAVPKVYAWEGNAVLMELIDAKELYRVRVENPDEVLDMILEEVAKFYHRGIVHGDLSQYNVLVSEEGIWIIDFPQSVEVGEEGWREILERDVRNIITYFSRTYRTEKDINSAIDRILQ 281
               SCOP domains d1zara1 A:2-90 Rio2 serine protein kinase N-terminal domain                              d1zara2 A:91-281 Rio2 serine prote      in k       inase C-terminal domain                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Rio2_N-1zarA01 A:7-88                                                             ----------------RIO1-1zarA02 A:105-2      75                                                                                                                                               ------ Pfam domains
         Sec.struct. author hhhhhhhh.hhhhhhhhhhhhh.......eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.....eeeehhhhhhhhhhhhhhhh....eeeeeeee...eeeeeeee...eeeeeeee..------....-------hhhhhhhhhhhhhhhhhhhh.......eeeee..eeeee....ee.hhh...hhhhhhhhhhhhhhhhhhh.ee........eeee..eeee......ee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zar A   2 NIAELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNRQKDYEGSTFTFIGLSLYSLHRLVRSGKVDAIGKLMGEGKESAVFNCYSEKFGECVVKFHKV------KVKE-------HFSVLAIRSARNEFRALQKLQGLAVPKVYAWEGNAVLMELIDAKELYRVRVENPDEVLDMILEEVAKFYHRGIVHGDLSQYNVLVSEEGIWIIDFPQSVEVGEEGWREILERDVRNIITYFSRTYRTEKDINSAIDRILQ 281
                                    11        21        31        41        51        61        71        81        91       101       111       121  |    131  |      -|      151       161       171       181       191       201       211       221       231       241       251       261       271       281
                                                                                                                                                    124    131  |     142                                                                                                                                           
                                                                                                                                                              134
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: PKinase (934)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIO2_ARCFU | O30245)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zar)
 

(-) 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
  1zar
    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
  RIO2_ARCFU | O30245
    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)
  (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
  RIO2_ARCFU | O30245
    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
        RIO2_ARCFU | O30245: 1tqi 1tqm 1tqp 1zao

(-) Related Entries Specified in the PDB File

1zao CRYSTAL STRUCTURE OF A.FULGIDUS RIO2 KINASE COMPLEXED WITH ATP AND MANGANESE IONS