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 YVH1 PHOSPHATASE DOMAIN FROM CHAETOMIUM THERMOPHILUM
 
Authors :  Y. L. Ahmed, I. Sinning
Date :  18 Oct 16  (Deposition) - 30 Nov 16  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribosome, Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Baler, Y. L. Ahmed, M. Kallas, M. Kornprobst, F. R. Calvino, M. Gnadig, M. Thoms, G. Stier, S. Ismail, S. Kharde, N. Castillo, S. Griesel, S. Bastuck, B. Bradatsch, E. Thomson, D. Flemming, I. Sinning, E. Hurt
Interaction Network Of The Ribosome Assembly Machinery From A Eukaryotic Thermophile.
Protein Sci. V. 26 327 2017
PubMed-ID: 27863450  |  Reference-DOI: 10.1002/PRO.3085

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: CTHT_0021070
    Organism Scientific: CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM DSM 1495
    Organism Taxid: 759272

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NO32Ligand/IonNITRATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:61 , CYS A:103 , ALA A:104 , MET A:105 , LYS A:107 , SER A:108 , ARG A:109binding site for residue NO3 A 301
2AC2SOFTWARETYR A:122 , PRO A:123 , TYR A:124 , ARG A:125binding site for residue NO3 A 302
3AC3SOFTWAREASP A:58 , ILE A:59 , GLN A:65 , ASP A:66 , HIS A:70 , HOH A:428 , HOH A:453binding site for residue GOL A 303
4AC4SOFTWARELYS A:128 , TRP A:167 , GLY A:170 , HOH A:405binding site for residue GOL A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M43)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M43)

(-) Exons   (0, 0)

(no "Exon" information available for 5M43)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee......eeeehhhhhhhhhhhhhhh..eeee.........hhhhhh.eeee..........hhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m43 A   2 ALNRIKGDDELFVGGVFGANRARLIKEHRITHILSVIDHTVDRENEAFRHVKHLSIDIDDMEDQDILIHLPKIVRFIDSGLRGIAVASPGVVLVHCAMGKSRSVTAIIAYLLWKYPYRFGKSDPNISAKEAVSRALEWVRETRPIAGPNDGFMRQLEMWWDMGCPADS 175
                                    11        21        31        41        51        61        71        81   ||   97       107       117       127       137       147       157       167        
                                                                                                              85|                                                                                   
                                                                                                               92
   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 5M43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M43)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO3  [ 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 5m43)
 

(-) 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
  5m43
    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
  G0S3H6_CHATD | G0S3H6
    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
  G0S3H6_CHATD | G0S3H6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5M43)

(-) Related Entries Specified in the PDB File

5m3q