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 :  APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (MONOCLINIC SPACE GROUP)
 
Authors :  M. Schacherl, S. M. Waltersperger, U. Baumann
Date :  24 Mar 13  (Deposition) - 27 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Askha Superfamily, Phosphotransfer, Pseudomurein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schacherl, S. M. Waltersperger, U. Baumann
Structural Characterization Of The Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 From Methanopyrus Kandleri
Acta Crystallogr. , Sect. D V. 69 2440 2013
PubMed-ID: 24311585  |  Reference-DOI: 10.1107/S0907444913022683

(-) Compounds

Molecule 1 - PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 190192
    Other Details: DSM6324
    Strain: AV19
    Synonym: PUTATIVE SUGAR KINASE MK0840

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3K6Ligand/IonPOTASSIUM ION
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:138 , ALA A:142 , PHE A:182 , GLY A:183 , ALA A:185 , SER A:243BINDING SITE FOR RESIDUE K A1351
02AC2SOFTWAREASP A:114 , ASP A:138 , GLY A:141 , PRO A:143 , ASP A:144 , HOH A:2055BINDING SITE FOR RESIDUE K A1352
03AC3SOFTWAREHOH A:2039 , ASP B:114 , ASP B:138 , GLY B:141 , PRO B:143 , ASP B:144BINDING SITE FOR RESIDUE K B1351
04AC4SOFTWAREASP B:138 , ALA B:142 , PHE B:182 , GLY B:183 , ALA B:185 , SER B:243BINDING SITE FOR RESIDUE K B1352
05AC5SOFTWAREARG B:66 , GLU B:67BINDING SITE FOR RESIDUE K B1353
06AC6SOFTWAREARG A:66 , GLU A:67BINDING SITE FOR RESIDUE K A1353
07AC7SOFTWAREGLU A:323 , GLU A:324 , LEU A:325 , ARG A:328 , HOH A:2146BINDING SITE FOR RESIDUE CL A1354
08AC8SOFTWAREGLU B:323 , GLU B:324 , ARG B:328 , HOH B:2162BINDING SITE FOR RESIDUE CL B1354
09AC9SOFTWAREARG A:307 , ARG A:308 , GLU A:311BINDING SITE FOR RESIDUE ACT A1355
10BC1SOFTWAREARG B:307 , ARG B:308 , GLU B:311BINDING SITE FOR RESIDUE ACT B1355

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BG8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:142 -Pro A:143
2Ala B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BG8)

(-) Exons   (0, 0)

(no "Exon" information available for 4BG8)

(-) 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:314
 aligned with Q8TX37_METKA | Q8TX37 from UniProtKB/TrEMBL  Length:358

    Alignment length:314
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346    
         Q8TX37_METKA    37 LTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEG 350
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhh..eeeeee..eeeeeeee..ee.....eeee.hhhhhhhhhhhhh........hhhhh..hhhhhhhhh..ee..ee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bg8 A  37 LTRVLGIQLGNTGTDYCVmNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPmIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAmAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDmDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEG 350
                                    46        56        66        76        86        96       106       116      |126       136       146       156       166  |    176       186       196       206       216       226       236       246       256       266       276       286   |   296       306       316       326       336       346    
                                             55-MSE                                                             123-MSE                                       169-MSE                                                                                                                  290-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with Q8TX37_METKA | Q8TX37 from UniProtKB/TrEMBL  Length:358

    Alignment length:314
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346    
         Q8TX37_METKA    37 LTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEG 350
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhh..eeeeee..eeeeeeee..ee.....eeee.hhhhhhhhhhhhh........hhhhh..hhhhhhhhh..ee..ee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bg8 B  37 LTRVLGIQLGNTGTDYCVmNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPmIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAmAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDmDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEG 350
                                    46        56        66        76        86        96       106       116      |126       136       146       156       166  |    176       186       196       206       216       226       236       246       256       266       276       286   |   296       306       316       326       336       346    
                                             55-MSE                                                             123-MSE                                       169-MSE                                                                                                                  290-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  (0, 0)

(no "SCOP Domain" information available for 4BG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BG8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8TX37_METKA | Q8TX37)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
biological process
    GO:0006040    amino sugar metabolic process    The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:142 - Pro A:143   [ RasMol ]  
    Ala B:142 - Pro B:143   [ 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 | 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
  4bg8
    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
  Q8TX37_METKA | Q8TX37
    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
  Q8TX37_METKA | Q8TX37
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8TX37_METKA | Q8TX37: 4bg9 4bga 4bgb

(-) Related Entries Specified in the PDB File

4bg9 APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (ORTHORHOMBIC SPACE GROUP)
4bga NUCLEOTIDE-BOUND OPEN FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI
4bgb NUCLEOTIDE-BOUND CLOSED FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI