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(-) Description

Title :  CRYSTAL STRUCTURE OF DESKC IN COMPLEX WITH AMP-PCP
 
Authors :  D. Albanesi, P. M. Alzari, A. Buschiazzo
Date :  12 Sep 08  (Deposition) - 15 Sep 09  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Four-Helix Bundle, Ghl Atpase Domain, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Albanesi, M. Martin, F. Trajtenberg, M. C. Mansilla, A. Haouz, P. M. Alzari, D. De Mendoza, A. Buschiazzo
Structural Plasticity And Catalysis Regulation Of A Thermosensor Histidine Kinase
Proc. Natl. Acad. Sci. Usa V. 106 16185 2009
PubMed-ID: 19805278  |  Reference-DOI: 10.1073/PNAS.0906699106

(-) Compounds

Molecule 1 - SENSOR KINASE (YOCF PROTEIN)
    ChainsA, B, C, D
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentENTIRE CYTOPLASMIC REGION
    GeneYOCF
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymDESK HISTIDINE KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1ACP3Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG3Ligand/IonMAGNESIUM ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , GLU A:289 , ASN A:293 , HIS A:297 , SER A:298 , ASP A:320 , THR A:323 , PHE A:324 , LYS A:325 , GLY A:326 , HIS A:335 , GLY A:336 , LEU A:337 , MG A:501BINDING SITE FOR RESIDUE ACP A 500
2AC2SOFTWAREHOH A:1 , GLU A:289 , ASN A:293 , ACP A:500BINDING SITE FOR RESIDUE MG A 501
3AC3SOFTWAREGLU B:289 , MG B:501BINDING SITE FOR RESIDUE ACP B 500
4AC4SOFTWAREGLU B:289 , ACP B:500BINDING SITE FOR RESIDUE MG B 501
5AC5SOFTWAREHOH D:3 , GLU D:289 , ASN D:293 , HIS D:297 , SER D:298 , ASP D:320 , THR D:323 , PHE D:324 , LYS D:325 , GLY D:326 , HIS D:335 , GLY D:336 , LEU D:337 , THR D:359 , MG D:501BINDING SITE FOR RESIDUE ACP D 500
6AC6SOFTWAREHOH D:3 , GLU D:289 , ASN D:293 , ACP D:500BINDING SITE FOR RESIDUE MG D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EHF)

(-) 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:179
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:186
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
           DESK_BACSU   182 RIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPN 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee.......-------hhhhhhhhhhhhh..eeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ehf A 182 RIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSmKGIRLKDELINIKQILEAADImFIYEEEKWPENISLLNENILSmCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGE-------HGLLGmRERLEFANGSLHIDTENGTKLTmAIPN 367
                                   191       201       211       221       231       241       251       261 |     271       281   |   291       301       311       321     |   -   |   341       351       361 |    
                                                                                     241-MSE               263-MSE               285-MSE                                   327     335    |                    363-MSE
                                                                                                                                                                                        340-MSE                       

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:143
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317   
           DESK_BACSU   178 EERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSD 320
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhh--.......----------hhhhhhhhhhhhhhhhh------...--------------.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehf B 178 EERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSmK-------LINIKQILEA--ImFIYEE----------NENILSmCLKEAVTNVV------TCR--------------SD 320
                                   187       197       207       217       227       237   ||    -  |    257 |  || 267|        - |     287       | -    | |  -         - | 
                                                                                         241-MSE  250      259  ||  268        279     |       295    302 |            319 
                                                                                          242                 262|                   285-MSE            304                
                                                                                                               263-MSE                                                     

Chain C from PDB  Type:PROTEIN  Length:57
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:57
                                   194       204       214       224       234       
           DESK_BACSU   185 RDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSM 241
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 3ehf C 185 RDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSm 241
                                   194       204       214       224       234      |
                                                                                  241-MSE

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:190
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367
           DESK_BACSU   178 EERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPN 367
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee...--.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee.......-------hhhhhhhhhhhh...eee.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehf D 178 EERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSmKGIRLKDELINIKQILEAADImFIYEE--WPENISLLNENILSmCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGE-------HGLLGmRERLEFANGSLHIDTENGTKLTmAIPN 367
                                   187       197       207       217       227       237   |   247       257     | 267|  |   277       287       297       307       317       327       337  |    347       357     | 367
                                                                                         241-MSE               263-MSE8  |           285-MSE                                   327     335    |                    363-MSE
                                                                                                                       271                                                                  340-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 3EHF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DESK_BACSU | O34757)
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: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:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    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:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    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:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DESK_BACSU | O347573ehg 3ehh 3ehj 3gie 3gif 3gig 5iuj 5iuk 5iul 5ium 5iun

(-) Related Entries Specified in the PDB File

3ehg 3ehh 3ehj