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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF KAIC S431E IN COMPLEX WITH FOLDSWITCH-STABILIZED KAIB FROM THERMOSYNECHOCOCCUS ELONGATUS
 
Authors :  R. Tseng, N. F. Goularte, A. Chavan, J. Luu, Y. Chang, J. Heilser, S. Trip A. Liwang, C. L. Partch
Date :  12 May 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Transcription Regulator, Foldswitch (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Tseng, N. F. Goularte, A. Chavan, J. Luu, S. E. Cohen, Y. G. Chang, J. Heisler, S. Li, A. K. Michael, S. Tripathi, S. S. Golden, A. Liwang, C. L. Partch
Structural Basis Of The Day-Night Transition In A Bacterial Circadian Clock.
Science V. 355 1174 2017
PubMed-ID: 28302851  |  Reference-DOI: 10.1126/SCIENCE.AAG2516

(-) Compounds

Molecule 1 - CIRCADIAN CLOCK PROTEIN KINASE KAIC
    Chains: A, C
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: KAIC, TLR0483
    Mutation: YES
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS (STRAIN BP-1)
    Organism Taxid: 197221
    Strain: BP-1
 
Molecule 2 - CIRCADIAN CLOCK PROTEIN KAIB
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KAIB, TLR0482
    Mutation: YES
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS (STRAIN BP-1)
    Organism Taxid: 197221
    Strain: BP-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:50 , THR A:51 , GLY A:52 , LYS A:53 , THR A:54 , LEU A:55 , GLU A:79 , PHE A:91 , ILE A:240 , LYS C:225 , LEU C:226 , ARG C:227 , GLY C:228 , THR C:229 , THR C:230binding site for residue ADP A 601
2AC2SOFTWARELYS A:225 , ARG A:227 , GLY A:228 , THR A:229 , THR A:230 , GLY C:50 , THR C:51 , GLY C:52 , LYS C:53 , THR C:54 , LEU C:55 , ASN C:87 , SER C:90 , PHE C:91 , ILE C:240binding site for residue ADP C 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr B:62 -Pro B:63
2Leu B:69 -Pro B:70
3Pro B:71 -Pro B:72
4Thr D:62 -Pro D:63
5Leu D:69 -Pro D:70
6Pro D:71 -Pro D:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JWQ)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeee.....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh..hhhhhh...eeeee...............hhhhhhhhhhhhhhhh..eeeee.hhhhhh.....hhhhhhhhhhhhhhhhhh.eeeeee...............eeeeeeeeee..eeeeeeeeeee.......eeee.ee...ee....................eeeeee...hhhhhhhhhhhhhhhhh..eeee....hhhhhh........hhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhh..hhhhhhhhhhhhhhhhhh...eeeeeeee...................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jwq A  19 VKKIPTMIEGFDDISHGGLPQGRTTLVSGTSGTGKTLFAVQFLYNGITIFNEPGIFVTFEESPQDIIKNALSFGWNLQSLIDQGKLFILDASPDPDGQEVAGDFDLSALIERIQYAIRKYKATRVSIDSVTAVFQQYDAASVVRREIFRLAFRLKQLGVTTIMTTEGPVARFGVEEFVSDNVVILRNVLEGERRRRTVEILKLRGTTHMKGEYPFTINNGINIFPLGASGVKTLDEMCGDSIILATGATGTGKTLLVSKFLETGCQQGERALLFAYEESRAQLSRNASSWGIDFEELERRGLLRIICAYPESAGLEDHLQIIKSEIADFKPSRVAIDSLSALARGVSNNAFRQFVIGVTGFAKQEEITGFFTNTTDTESHIETITDTILRGEMSRAINVFKMRGSWHDKGIRE 469
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     ||193       203       213       223       233       243       266       281       291       301       311       321       331       341       351       361       371       381       391       401       411     ||429       446       456       466   
                                                                                                                                                                                               184|                                                          251|       275|                                                                                                                                     417|         438|                       
                                                                                                                                                                                                190                                                           265        281                                                                                                                                      426          446                       


Chain B from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhhhhhh..........eee....hhhhhhh......eeee......eeee....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5jwq B   7 TAVLKLYVAGNTPNSVRALKTLNNILEKEFKGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPPPVRRIIGDLSNREKVLAGLDLLA  94
                                    16        26        36        46        56        66        76        86        


Chain C from PDB  Type:PROTEIN  Length:408
                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................eeeee.....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh.....hhhhhhh...eeee........ee.....hhhhhhhhhhhhhhhh..eeeee.hhhhhh.....hhhhhhhhhhhhhhhhh..eeeeee.............eeeeeeeeee..eeeeeeeeeee........eeeeee...eee..........................eeeeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhh..eeee.hhhhhhh.........hhhhhhhhhhh...eeeeeeee...................eee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jwq C  19 VKKIPTMIEGFDDISHGGLPQGRTTLVSGTSGTGKTLFAVQFLYNGITIFNEPGIFVTFEESPQDIIKNALSFGWNLQSLIDQGKLFILDASPDPDGQEVAGDFDLSALIERIQYAIRKYKATRVSIDSVTAVFQQYDAASVVRREIFRLAFRLKQLGVTTIMTTEVARFGVEEFVSDNVVILRNVLEGERRRRTVEILKLRGTTHMKGEYPFTINNGINIFPLGANVRVSSGVKTLDEMCGFFKDSIILATGATGTGKTLLVSKFLETGCQQGERESRAQLSRNASSWGIDFEELERPESAGLEDHLQIIKSEIADFKPSRVAIDSLSALARGVSNNAFRQFVIGVTGFAKQEEITGFFTNTTDQFMGSNSITESHIETITDTILLLQMSRAINVFKMRGSWHDKGI 467
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     ||195       205       215       225       235       245     ||263       273||     285       295       305     ||322       332       352       362       372       382       392       402       412       422       432       449       459        
                                                                                                                                                                                               184|                                                        251|           274|                               311|                  340|                                                                                       441|                  
                                                                                                                                                                                                192                                                         260            277                                319                   351                                                                                        449                  


Chain D from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...hhhhhhhhhhhhhhhh..........eee....hhhhhhh......eee.........ee....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5jwq D   6 KTAVLKLYVAGNTPNSVRALKTLNNILEKEFKGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPPPVRRIIGDLSNREKVLAGLDLLA  94
                                    15        25        35        45        55        65        75        85
   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 5JWQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 21)

Asymmetric Unit(hide GO term definitions)

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu B:69 - Pro B:70   [ RasMol ]  
    Leu D:69 - Pro D:70   [ RasMol ]  
    Pro B:71 - Pro B:72   [ RasMol ]  
    Pro D:71 - Pro D:72   [ RasMol ]  
    Thr B:62 - Pro B:63   [ RasMol ]  
    Thr D:62 - Pro D:63   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5jwq
    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
  KAIB_THEEB | Q79V61
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KAIC_THEEB | Q79V60
    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)
  2.7.11.1
    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
  KAIB_THEEB | Q79V61
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KAIC_THEEB | Q79V60
    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
        KAIB_THEEB | Q79V61: 1vgl 2qke 5jwo 5jwr 5jyt 5jyv
        KAIC_THEEB | Q79V60: 1suy 1sv1 4o0m 5jwo 5jwr

(-) Related Entries Specified in the PDB File

5jwo 5jwr