Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE SUGAR KINASE (CHU_1875) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.65 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Mar 11  (Deposition) - 18 May 11  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ribonuclease H-Like Motif, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi- Biology, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Hypothetical Sugar Kinase (Chu_1875) From Cytophaga Hutchinsonii Atcc 33406 At 1. 65 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL SUGAR KINASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLK, CHU_1875
    Organism Scientific: CYTOPHAGA HUTCHINSONII
    Organism Taxid: 269798
    Strain: ATCC 33406

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 22)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3R8E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R8E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R8E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R8E)

(-) Exons   (0, 0)

(no "Exon" information available for 3R8E)

(-) 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:301
 aligned with Q11TX3_CYTH3 | Q11TX3 from UniProtKB/TrEMBL  Length:302

    Alignment length:301
                             1                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
         Q11TX3_CYTH3     - -MILGIDVGGTSVKFGLVTPEGEIQNATRFMTADWVNGIGFVESMKLEIGNFLKQYPIVKGVGIGWPGLVSLDRTKVILLPNIPSVVNVPIVEILRSEFPHIHFKIENDAKCAALGEYYFGENKRMQTFILLALGTGVGSGVMMNGKLFIGGRGNGTEVGHMLTTRGKSLENQVGINHLIAYTHEQLALDVAKKSSLHTIAELSPKVIADHAAQGDALALAVWADIGTIIGESLVNIVRVMDLNNILLGGGISGAFDYFVPNLKKAMLEHLPTYYTDDMYIGKATLENDAGLLGAAGLIME 300
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----ROK-3r8eA01 A:4-176                                                                                                                                                          ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..ee......eee..........hhhhhhhhhh...eeeeeehhhhhhhhhhhhh.......eeeeee...eeeeeee..ee.........hhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r8e A   0 GmILGIDVGGTSVKFGLVTPEGEIQNATRFmTADWVNGIGFVESmKLEIGNFLKQYPIVKGVGIGWPGLVSLDRTKVILLPNIPSVVNVPIVEILRSEFPHIHFKIENDAKCAALGEYYFGENKRmQTFILLALGTGVGSGVmmNGKLFIGGRGNGTEVGHmLTTRGKSLENQVGINHLIAYTHEQLALDVAKKSSLHTIAELSPKVIADHAAQGDALALAVWADIGTIIGESLVNIVRVmDLNNILLGGGISGAFDYFVPNLKKAmLEHLPTYYTDDmYIGKATLENDAGLLGAAGLImE 300
                             |       9        19        29|       39    |   49        59        69        79        89        99       109       119     | 129       139  ||   149       159 |     169       179       189       199       209       219       229       239|      249       259      |269       279       289       299 
                             |                           30-MSE        44-MSE                                                                          125-MSE          142-MSE            161-MSE                                                                        240-MSE                   266-MSE     278-MSE              299-MSE
                             1-MSE                                                                                                                                       143-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 3R8E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R8E)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q11TX3_CYTH3 | Q11TX3)
molecular function
    GO:0004340    glucokinase activity    Catalysis of the reaction: ATP + D-glucose = ADP + D-glucose-6-phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0051156    glucose 6-phosphate metabolic process    The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
    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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3r8e)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r8e)
 
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 | Biol. Unit 1 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
  3r8e
    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
  Q11TX3_CYTH3 | Q11TX3
    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
  Q11TX3_CYTH3 | Q11TX3
    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 3R8E)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R8E)