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

(-) Description

Title :  CRYSTAL STRUCTURE OF CODY FROM STAPHYLOCOCCUS AUREUS WITH GTP AND ILE
 
Authors :  A. Han, K. Y. Hwang
Date :  24 Nov 15  (Deposition) - 14 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gtp Sensing, Pleiotropic Transcription Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Han, H. R. Kang, J. Son, D. H. Kwon, S. Kim, W. C. Lee, H. K. Song, M. J. Song, K. Y. Hwang
The Structure Of The Pleiotropic Transcription Regulator Cody Provides Insight Into Its Gtp-Sensing Mechanism
Nucleic Acids Res. V. 44 9483 2016
PubMed-ID: 27596595  |  Reference-DOI: 10.1093/NAR/GKW775

(-) Compounds

Molecule 1 - GTP-SENSING TRANSCRIPTIONAL PLEIOTROPIC REPRESSOR CODY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CODY, SAHV_1245
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN MU3 / ATCC 700698)
    Organism Taxid: 418127
    Strain: MU3 / ATCC 700698

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ILE2Mod. Amino AcidISOLEUCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:61 , MET A:65 , THR A:96 , VAL A:97 , PHE A:98 , PRO A:99 , PRO A:100 , HOH A:440 , HOH A:462 , HOH A:485binding site for residue ILE A 301
2AC2SOFTWAREVAL A:22 , ASP A:23 , PHE A:24 , SER A:43 , ARG A:44 , ARG A:45 , LYS A:47 , LEU A:49 , GLU A:153 , ILE A:154 , ARG A:156 , GLU A:157 , LYS A:158 , GLU A:161 , HOH A:401 , HOH A:410 , HOH A:447 , HOH A:449binding site for residue GTP A 302
3AC3SOFTWAREARG B:61 , PRO B:72 , TYR B:75 , THR B:96 , VAL B:97 , PHE B:98 , PRO B:100 , HOH B:435 , HOH B:442 , HOH B:462binding site for residue ILE B 301
4AC4SOFTWARETYR A:181 , VAL B:22 , PHE B:24 , SER B:43 , ARG B:44 , ARG B:45 , LYS B:47 , LEU B:49 , GLU B:153 , GLU B:157 , LYS B:158 , HOH B:415 , HOH B:419 , HOH B:423 , HOH B:463 , HOH B:472 , HOH B:473 , HOH B:477binding site for residue GTP B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EY1)

(-) Exons   (0, 0)

(no "Exon" information available for 5EY1)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eeeeee....eeeee.hhhhhhhhhhhhhhhh..hhhhhhhhh.....eeee.........hhhhhhhh...eeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eee...eee...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey1 A   1 MSLLSKTRELNTLLQKHKGIAVDFKDVAQTISSVTVTNVFIVSRRGKILGSSLNELLKSQRIIQMLEERHIPSEYTERLMEVKQTESNIDIDNVLTVFPPENRELFIDSRTTIFPILGGGERLGTLVLGRVHDDFNENDLVLGEYAATVIGMEILREKHSEVEKEARDKAAITMAINSLSYSEKEAIEHIFEELGEGLLIITRSVIVNALRKLESAGVIESRTFIKVKKEKFLDELEKSKI 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    || 202|      221       231 ||    247       257|
                                                                                                                                                                                                                            195| 202|                  233|              257|
                                                                                                                                                                                                                             198  212                   240               301


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eeeeee....eeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhh....eeee.........hhhhh......eeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey1 B   1 MSLLSKTRELNTLLQKHKGIAVDFKDVAQTISSVTVTNVFIVSRRGKILGSSLNELLKSQRIIQMLEERHIPSEYTERLMEVKQTESNIDIDNVLTVFPPENRELFIDSRTTIFPILGGGERLGTLVLGRVHDDFNENDLVLGEYAATVIGMEILREKHSEVEKEARDI 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       ||
                                                                                                                                                                                                 168|
                                                                                                                                                                                                  301
   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 5EY1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EY1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EY1)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ILE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ey1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  5ey1
    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
  CODY_STAA1 | A7X1N2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CODY_STAA8 | Q2FZ27
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CODY_STAA1 | A7X1N2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CODY_STAA8 | Q2FZ27
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CODY_STAA1 | A7X1N2: 5ey0
        CODY_STAA8 | Q2FZ27: 5ey0

(-) Related Entries Specified in the PDB File

5ey0 5ey2