Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF A HISTIDINE KINASE-RESPONSE REGULATOR COMPLEX SHEDS LIGHT INTO TWO-COMPONENT SIGNALING AND REVEALS A NOVEL CIS AUTOPHOSPHORYLATION MECHANISM
 
Authors :  P. Casino, V. Rubio, A. Marina
Date :  11 Mar 09  (Deposition) - 27 Oct 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta-Sheet, Surrounded By Alpha Helices, Both Sides, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Casino, V. Rubio, A. Marina
Structural Insight Into Partner Specificity And Phosphoryl Transfer In Two-Component Signal Transduction
Cell(Cambridge, Mass. ) V. 139 325 2009
PubMed-ID: 19800110  |  Reference-DOI: 10.1016/J.CELL.2009.08.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESPONSE REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PET21D
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RESPONSE REGULATOR RR468

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1BFD4Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG4Ligand/IonMAGNESIUM ION
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , BFD A:53 , MET A:55 , HOH A:148 , HOH A:368BINDING SITE FOR RESIDUE MG A 123
2AC2SOFTWAREARG A:100 , GLU A:115 , HIS A:118 , LEU A:119 , HOH A:367 , HOH A:436 , HOH A:490 , HOH A:651 , GLY D:87 , GLU D:88 , HOH D:137BINDING SITE FOR RESIDUE SO4 A 124
3AC3SOFTWAREASP B:10 , BFD B:53 , MET B:55 , HOH B:149 , HOH B:369BINDING SITE FOR RESIDUE MG B 123
4AC4SOFTWAREGLY B:86 , GLY B:87 , ARG B:100 , HIS B:118 , LEU B:119 , GLU B:122 , HOH B:159 , HOH B:171 , HOH B:563BINDING SITE FOR RESIDUE SO4 B 124
5AC5SOFTWAREASP C:10 , BFD C:53 , MET C:55 , HOH C:166 , HOH C:194BINDING SITE FOR RESIDUE MG C 123
6AC6SOFTWAREGLY A:87 , GLU A:88 , HOH A:276 , ARG C:100 , GLU C:115 , HIS C:118 , HOH C:141 , HOH C:154BINDING SITE FOR RESIDUE SO4 C 124
7AC7SOFTWAREASP D:10 , BFD D:53 , MET D:55 , HOH D:157 , HOH D:174BINDING SITE FOR RESIDUE MG D 123
8AC8SOFTWAREGLY C:87 , GLU C:88 , HOH C:241 , ARG D:100 , GLU D:115 , HIS D:118 , HOH D:165 , HOH D:459BINDING SITE FOR RESIDUE SO4 D 124
9AC9SOFTWAREGLY A:98 , ARG A:100 , HOH A:140 , HOH A:323 , HOH A:427 , HOH A:477 , HOH A:596 , LYS D:85 , GLY D:86 , ARG D:104BINDING SITE FOR RESIDUE SO4 D 125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GL9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:105 -Pro A:106
2Lys B:105 -Pro B:106
3Lys C:105 -Pro C:106
4Lys D:105 -Pro D:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GL9)

(-) Exons   (0, 0)

(no "Exon" information available for 3GL9)

(-) 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:120
 aligned with Q9WYT9_THEMA | Q9WYT9 from UniProtKB/TrEMBL  Length:122

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q9WYT9_THEMA     2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
               SCOP domains d3gl9a_ A: automated matches                                                                                             SCOP domains
               CATH domains 3gl9A00 A:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....eeee.......hhhhhhhhhhh........eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gl9 A   2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
                                    11        21        31        41        51 |      61        71        81        91       101       111       121
                                                                              53-BFD                                                                


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q9WYT9_THEMA | Q9WYT9 from UniProtKB/TrEMBL  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q9WYT9_THEMA     2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLNE 122
               SCOP domains d3gl9b_ B: automated matches                                                                                              SCOP domains
               CATH domains 3gl9B00 B:2-122  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gl9 B   2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLNE 122
                                    11        21        31        41        51 |      61        71        81        91       101       111       121 
                                                                              53-BFD                                                                 


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q9WYT9_THEMA | Q9WYT9 from UniProtKB/TrEMBL  Length:122

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q9WYT9_THEMA     2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
               SCOP domains d3gl9c_ C: automated matches                                                                                             SCOP domains
               CATH domains 3gl9C00 C:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhh.....eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gl9 C   2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
                                    11        21        31        41        51 |      61        71        81        91       101       111       121
                                                                              53-BFD                                                                


Chain D from PDB  Type:PROTEIN  Length:120
 aligned with Q9WYT9_THEMA | Q9WYT9 from UniProtKB/TrEMBL  Length:122

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         Q9WYT9_THEMA     2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
               SCOP domains d3gl9d_ D: automated matches                                                                                             SCOP domains
               CATH domains 3gl9D00 D:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....eeee.......hhhhhhhhhhh........eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gl9 D   2 SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
                                    11        21        31        41        51 |      61        71        81        91       101       111       121
                                                                              53-BFD
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GL9)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9WYT9_THEMA | Q9WYT9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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.
cellular component
    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.

 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
    BFD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Lys A:105 - Pro A:106   [ RasMol ]  
    Lys B:105 - Pro B:106   [ RasMol ]  
    Lys C:105 - Pro C:106   [ RasMol ]  
    Lys D:105 - Pro D:106   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  3gl9
    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
  Q9WYT9_THEMA | Q9WYT9
    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
  Q9WYT9_THEMA | Q9WYT9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9WYT9_THEMA | Q9WYT9: 3dge 3dgf 4ja2 4jas 4jav

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GL9)