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

(-) Description

Title :  CRYSTAL STRUCTURE OF CODY FROM BACILLUS CEREUS
 
Authors :  A. Han, W. C. Lee, J. Son, S. H. Kim, K. Y. Hwang
Date :  24 Nov 15  (Deposition) - 14 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gtp-Sensing, Pleiotropic Transcription Regulator, Auto-Inhibition, 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, D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CODY, BC_3826
    Organism Scientific: BACILLUS CEREUS (STRAIN ATCC 14579 / DSM 31)
    Organism Taxid: 226900
    Strain: ATCC 14579 / DSM 31

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 29)

Asymmetric/Biological Unit (1, 29)
No.NameCountTypeFull Name
1MSE29Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5EY2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EY2)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Lys A:20 -Pro A:21
2Val A:100 -Glu A:101
3Pro B:21 -Val B:22
4Ala D:17 -Ala D:18
5Ala D:18 -Gly D:19
6Ala D:67 -Glu D:68
7Lys D:255 -Leu D:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EY2)

(-) Exons   (0, 0)

(no "Exon" information available for 5EY2)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeee....eeeee......hhhhhhhhhh...hhhhhhhhhhh...eeee....................eeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh..eeee.....eeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey2 A   1 mELLAKTRKLNALLQSAAGKPVNFREmSDTmCEVIEANVFVVSRRGKLLGYAIHQQIENERmKQmLAERQFPEEYTQSLFNITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGmEILREKAEEIEEEARSKAVVQmAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGmTYIKVLNDKFLQELAKL 256
                            |       10        20      | 30|       40        50        60 |  |   70        80        90       100       110       120       130       140       150 |     160       170   |   180       190       200       210       220       230      |242       252    
                            |                        27-MSE                             62-MSE                                                                                   152-MSE               174-MSE                                                        237-MSE             
                            1-MSE                        31-MSE                            65-MSE                                                                                                                                                                      240                


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....eeeee........hhhhhh.....hhhhhhhh..............................eeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh...........eee....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey2 B   1 mELLAKTRKLNALLQSAAGKPVNFREmSDTmCEVIEANVFVVSRRGKLLGYAIHQQIENERmKQmLAERQFPEEYTQSLFNITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGmEILREKAEEIEEEARSKAVVQmAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGmTYIKVLNDKFLQELAKL 256
                            |       10        20      | 30|       40        50        60 |  |   70        80        90       100       110       120       130       140       150 |     160       170   |   180       190       200       210       220       230      |242       252    
                            1-MSE                    27-MSE                             62-MSE                                                                                   152-MSE               174-MSE                                                        237-MSE             
                                                         31-MSE                            65-MSE                                                                                                                                                                      240                


Chain C from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhh..eeeee.....eeeee.....................................eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eehhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.hhh.eeeee...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey2 C   1 mELLAKTRKLNALLQSAAGKPFREmSDTmCEVIEANVFVVSRRGKLLGYAIHQQIENERmKLAERQFPEEYQSLFNITETSSNLDGQGLTTIVPIVGGGTLVLARLGQEFLDDDLILAEYSSTVVGmEILREKAEEIEEEARSKAVVQmAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGmKGTYIKVLNDKFLQELAKL 256
                            |       10        20||  |   32        42        52        62||      74||      85    || 111       125       135       145      |155       165       175       185       195       205       215       225       235 |     245       255 
                            1-MSE              21|  |   |                             62-MSE     75|           90|         119|                         152-MSE               174-MSE                                                        237-MSE               
                                                24  |   |                              63|        77           107          124                                                                                                                                    
                                                   27-MSE                               66                                                                                                                                                                         
                                                       31-MSE                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh........hhhhhhhhhhhh..eeeee.......eeee.............hhhhhhhhhh.............eeee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeee..hhhhhhh...hhhhhhhhhhhhh......ee.....eeee....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ey2 D   4 LAKTRKLNALLQSAAGKPVNFREmSDTmCEVIEANVFVVSRRGKLLGYAIHQQIENmLAERQFPEEYTQSLFNITETSSNLDVGLTTIVPIVGGTLVLARLGQEFLDDDLILAEYSSTVVGmEILREKAEEIEEEARSKAVVQmAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGmKGTYIKVLNDKFLQELAKL 256
                                    13        23   |   |33        43        53     || 68        78        88  ||   115  ||   130       140       150 |     160       170   |   180       190       200       210       220       230      |240       250      
                                                  27-MSE                          59|                        91|      118|                         152-MSE               174-MSE                                                        237-MSE               
                                                      31-MSE                       65-MSE                    109       124
   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 5EY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EY2)

(-) Gene Ontology  (8, 8)

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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5ey2)
 
  Cis Peptide Bonds
    Ala D:17 - Ala D:18   [ RasMol ]  
    Ala D:18 - Gly D:19   [ RasMol ]  
    Ala D:67 - Glu D:68   [ RasMol ]  
    Lys A:20 - Pro A:21   [ RasMol ]  
    Lys D:255 - Leu D:256   [ RasMol ]  
    Pro B:21 - Val B:22   [ RasMol ]  
    Val A:100 - Glu A:101   [ RasMol ]  
 

(-) 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 ](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
  5ey2
    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_BACCR | Q819X8
    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_BACCR | Q819X8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5EY2)

(-) Related Entries Specified in the PDB File

5ey0 5ey1