Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE TRANSFERASE PH0793 FROM PYROCOCCUS HORIKOSHII
 
Authors :  C. Chang, T. Skarina, A. Savchenko, A. Edwards, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  09 Oct 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Pyrococcus Horikoshii, Transferase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, T. Skarina, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Protein Ph0793 From Pyrococcus Horikoshii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TRANSFERASE PH0793
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3) DERIVATIVES
    Expression System Taxid: 469008
    Gene: PH0793
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K6R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6R)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Mse A:232 -Pro A:233
2Glu A:235 -Pro A:236
3Ala A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM5_TYW2PS51684 SAM-dependent methyltransferase TRM5/TYW2-type domain profile.TYW2_PYRHO30-277  1A:30-277

(-) Exons   (0, 0)

(no "Exon" information available for 3K6R)

(-) 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:262
 aligned with TYW2_PYRHO | O58523 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:273
                                    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   
           TYW2_PYRHO     6 IKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPLRPELEPYKHRIAEVYAEVLGVKTVLRKGHIHGETRKPDYELLYGSDTVTVHVENGIKYKLDVAKIMFSPANVKERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILMGYVVRTHEFIPKALSIAKDGAIIHYHNTVPEKLMPREPFETFKRITKEYGYDVEKLNELKIKRYAPGVWHVVLDLRVFKS 278
               SCOP domains d3k6ra_ A: Hypothetical protein PH07 93                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhh....eee..eeee..-..hhhhhhhhhhhhhhhhh..eeee..----------.eeee....eeeeee..eeeeee......hhhhhhhhhhhhhhh....eeee.......hhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeee............eeeeee....hhhhhhhhhhhheeeeeeeeeeeeee.hhh...hhhhhhhhhhhh..eeeeeeeeeeeee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SAM_MT_TRM5_TYW2  PDB: A:30-277 UniProt: 30-277                                                                                                                                                                                                         - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6r A   6 IKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPL-PELEPYKHRIAEVYAEVLGVKTVLRKG----------YELLYGSDTVTVHVENGIKYKLDVAKImFSPANVKERVRmAKVAKPDELVVDmFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFLVENIHLNKVEDRmSAYNmDNRDFPGENIADRILmGYVVRTHEFIPKALSIAKDGAIIHYHNTVPEKLmPREPFETFKRITKEYGYDVEKLNELKIKRYAPGVWHVVLDLRVFKS 278
                                    15        25        35     | |45        55        65   |     -    |   85        95       105 |     115   |   125      |135       145       155       165       175 |    |185       195  |    205       215       225      |235       245       255       265       275   
                                                              41 |                        69         80                        107-MSE     119-MSE      132-MSE                                      177-MSE|             198-MSE                           232-MSE                                          
                                                                43                                                                                                                                        182-MSE
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0 ; only for superseded entry 2FRN: 2,2)

(no "CATH Domain" information available for 3K6R, only for superseded entry 2FRN replaced by 3K6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K6R)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TYW2_PYRHO | O58523)
molecular function
    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.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3k6r)
 
  Cis Peptide Bonds
    Ala A:263 - Pro A:264   [ RasMol ]  
    Glu A:235 - Pro A:236   [ RasMol ]  
    Mse A:232 - Pro A:233   [ 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 ](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
  3k6r
    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
  TYW2_PYRHO | O58523
    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
  TYW2_PYRHO | O58523
    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
        TYW2_PYRHO | O58523: 3a25 3a26

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K6R)