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

(-) Description

Title :  CHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN METHYLTRANSFERASE CHER
 
Authors :  S. Djordjevic, A. M. Stock
Date :  05 May 98  (Deposition) - 25 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,T
Keywords :  Methyltransferase, Peptide Binding, Chemotaxis Receptor, Complex (Methyltransferase/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Djordjevic, A. M. Stock
Chemotaxis Receptor Recognition By Protein Methyltransferase Cher.
Nat. Struct. Biol. V. 5 446 1998
PubMed-ID: 9628482  |  Reference-DOI: 10.1038/NSB0698-446
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHEMOTAXIS RECEPTOR METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.80
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPME43
    Expression System StrainHB101
    Expression System Taxid562
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602
    SynonymCHER, CHEMOTAXIS PROTEIN METHYLTRANSFERASE
 
Molecule 2 - CHEMOTAXIS RECEPTOR
    ChainsT
    EngineeredYES
    FragmentC-TERMINAL PENTAPEPTIDE, ACETYLATED ASN-TRP-GLU- THR-PHE
    SynonymTAR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CO1Ligand/IonCOBALT (II) ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:114 , HIS A:192 , HOH A:388 , HOH T:26 , HOH T:27 , HOH T:92BINDING SITE FOR RESIDUE CO A 300
2AC2SOFTWAREALA A:38 , THR A:90 , THR A:91 , ASN A:92 , LEU A:93 , THR A:94 , ARG A:98 , ALA A:123 , SER A:125 , GLU A:129 , ASP A:154 , ILE A:155 , ASP A:156 , VAL A:211 , ASN A:212 , LEU A:213 , ARG A:230 , ASN A:231 , VAL A:232 , PHE A:236 , HOH A:327 , HOH A:378BINDING SITE FOR RESIDUE SAH A 287
3COBUNKNOWNHIS A:192 , HIS A:114CO BINDING SITE IS FORMED BY HIS 192 AND HIS 114 OF THE SYMMETRY RELATED MOLECULE. THIS IS AN ARTIFACT OF THE CRYSTALLIZATION AND HAS NO PHYSIOLOGICAL SIGNIFICANCE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BC5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BC5)

(-) Exons   (0, 0)

(no "Exon" information available for 1BC5)

(-) 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:269
 aligned with CHER_SALTY | P07801 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:269
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275         
           CHER_SALTY    16 MTQRLALSDAHFRRICQLIYQRAGIVLADHKRDMVYNRLVRRLRALGLDDFGRYLSMLEANQNSAEWQAFINALTTNLTAFFREAHHFPILAEHARRRHGEYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKARSGIYRLSELKTLSPQQLQRYFMRGTGPHEGLVRVRQELANYVEFSSVNLLEKQYNVPGPFDAIFCRNVMIYFDKTTQEDILRRFVPLLKPDGLLFAGHSENFSNLVREFSLRGQTVYALS 284
               SCOP domains d1bc5a1 A:16-91                                                             d1bc5a2 A:92-284 Chemotaxis receptor methyltransferase CheR, C-terminal domain                                                                                                                    SCOP domains
               CATH domains 1bc5A01 A:16-90 Chemotaxis Receptor Methyltransferase Cher, domain 1       1bc5A02 A:91-284 Vaccinia Virus protein VP39                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhh..........hhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh......eeeeeee..hhhhhhhhh.eeehhh.....hhhhhhheee..hhh..eeee.hhhhhheeeee...............eeee...hhh..hhhhhhhhhhhhhh.....eeee...................eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bc5 A  16 MTQRLALSDAHFRRICQLIYQRAGIVLADHKRDMVYNRLVRRLRALGLDDFGRYLSMLEANQNSAEWQAFINALTTNLTAFFREAHHFPILAEHARRRHGEYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKARSGIYRLSELKTLSPQQLQRYFMRGTGPHEGLVRVRQELANYVEFSSVNLLEKQYNVPGPFDAIFCRNVMIYFDKTTQEDILRRFVPLLKPDGLLFAGHSENFSNLVREFSLRGQTVYALS 284
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275         

Chain T from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1bc5 T   0 xNWETF   5
                            |     
                            0-ACE 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BC5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHER_SALTY | P07801)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008983    protein-glutamate O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamate = S-adenosyl-L-homocysteine + protein L-glutamate 5-methyl ester; this reaction is the methylation of peptidyl-L-glutamate to form peptidyl-L-glutamate 5-methyl ester.
    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:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

 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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    COB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:222 - Pro A:223   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1bc5
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CHER_SALTY | P07801
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.80
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CHER_SALTY | P07801
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CHER_SALTY | P078011af7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BC5)