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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORYLATED DESKC IN COMPLEX WITH AMP-PCP
 
Authors :  F. Trajtenberg, D. Albanesi, P. M. Alzari, A. Buschiazzo, D. De Mendoz
Date :  05 Mar 09  (Deposition) - 15 Sep 09  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Four-Helix Bundle, Ghl Atpase Domain, Cell Membrane, Kinase, Membrane, Phosphoprotein, Transferase, Transmembrane, Two-Component Regulatory System (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 HISTIDINE KINASE DESK
    ChainsA
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE32
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentENTIRE CYTOPLASMIC REGION
    GeneYOCF
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
 
Molecule 2 - SENSOR HISTIDINE KINASE DESK
    ChainsB
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE32
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentENTIRE CYTOPLASMIC REGION
    GeneYOCF
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    Other DetailsPHOSPHORYLATED ENTIRE CYTOPLASMIC REGION

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMG A:1 , GLU A:289 , ASN A:293 , VAL A:294 , HIS A:297 , SER A:298 , ASP A:320 , THR A:323 , PHE A:324 , LYS A:325 , HIS A:335 , GLY A:336 , LEU A:337 , THR A:359BINDING SITE FOR RESIDUE ACP A 1303
2AC2SOFTWAREGLU A:289 , ASN A:293 , ACP A:1303BINDING SITE FOR RESIDUE MG A 1
3AC3SOFTWAREMG B:1 , GLU B:289 , ASN B:293 , VAL B:294 , HIS B:297 , SER B:298 , THR B:323 , PHE B:324 , LYS B:325 , GLY B:334 , HIS B:335 , GLY B:336 , LEU B:337 , THR B:359BINDING SITE FOR RESIDUE ACP B 1303
4AC4SOFTWAREGLU B:289 , ASN B:293 , ACP B:1303BINDING SITE FOR RESIDUE MG B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GIG)

(-) 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:212
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:214
                                   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    
           DESK_BACSU   155 KERERLEEKLEDANERIAELVKLEERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPNN 368
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...........h--hhhhhhhhhhhhh..eeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gig A 155 KERERLEEKLEDANERIAELVKLEERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFS--HGLLGMRERLEFANGSLHIDTENGTKLTMAIPNN 368
                                   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       | -|      344       354       364    
                                                                                                                                                                                                           332  |                                 
                                                                                                                                                                                                              335                                 

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with DESK_BACSU | O34757 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:205
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363     
           DESK_BACSU   164 LEDANERIAELVKLEERQRIARDLHDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPNN 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee..............hhhhhhhhhhhhh..eeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gig B 164 LEDANERIAELVKLEERQRIARDLhDTLGQKLSLIGLKSDLARKLIYKDPEQAARELKSVQQTARTSLNEVRKIVSSMKGIRLKDELINIKQILEAADIMFIYEEEKWPENISLLNENILSMCLKEAVTNVVKHSQAKTCRVDIQQLWKEVVITVSDDGTFKGEENSFSKGHGLLGMRERLEFANGSLHIDTENGTKLTMAIPNN 368
                                   173       183    |  193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363     
                                                  188-NEP                                                                                                                                                                                

   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 3GIG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | O347573ehf 3ehg 3ehh 3ehj 3gie 3gif 5iuj 5iuk 5iul 5ium 5iun

(-) Related Entries Specified in the PDB File

3ehf 3gie 3gif