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 N-TERMINAL DOMAIN OF KAIC
 
Authors :  J. Abe, T. B. Hiyama, A. Mukaiyama, S. Son, S. Akiyama
Date :  29 May 14  (Deposition) - 01 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abe, T. B. Hiyama, A. Mukaiyama, S. Son, T. Mori, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, S. Akiyama
Circadian Rhythms. Atomic-Scale Origins Of Slowness In The Cyanobacterial Circadian Clock.
Science V. 349 312 2015
PubMed-ID: 26113637  |  Reference-DOI: 10.1126/SCIENCE.1261040

(-) Compounds

Molecule 1 - CIRCADIAN CLOCK PROTEIN KINASE KAIC
    Chains: A, B, C
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-253
    Gene: KAIC, SYNPCC7942_1216, SEE0011
    Organism Scientific: SYNECHOCOCCUS ELONGATUS (STRAIN PCC 7942)
    Organism Taxid: 1140
    Strain: PCC 7942

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1ANP3Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CL3Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ANP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:48 , GLY A:49 , THR A:50 , GLY A:51 , LYS A:52 , THR A:53 , LEU A:54 , SER A:89 , PHE A:90 , ARG A:218 , ILE A:239 , THR A:240 , ASP A:241 , MG A:302 , HOH A:422 , HOH A:423 , HOH A:424 , HOH A:426 , HOH A:467 , PHE B:199 , LYS B:224 , LEU B:225 , ARG B:226 , THR B:228 , HIS B:230 , LYS B:232 , HOH B:418 , HOH B:450binding site for residue ANP A 301
2AC2SOFTWARETHR A:53 , ANP A:301 , HOH A:422 , HOH A:423 , HOH A:424binding site for residue MG A 302
3AC3SOFTWAREARG A:218 , ILE A:239binding site for residue CL A 303
4AC4SOFTWARESER B:48 , GLY B:49 , THR B:50 , GLY B:51 , LYS B:52 , THR B:53 , LEU B:54 , SER B:89 , PHE B:90 , ARG B:218 , ILE B:239 , THR B:240 , ASP B:241 , MG B:302 , HOH B:410 , HOH B:411 , HOH B:412 , HOH B:477 , PHE C:199 , LYS C:224 , LEU C:225 , ARG C:226 , THR C:228 , HIS C:230 , HOH C:442 , HOH C:454binding site for residue ANP B 301
5AC5SOFTWARETHR B:53 , ANP B:301 , HOH B:410 , HOH B:411 , HOH B:412binding site for residue MG B 302
6AC6SOFTWAREARG B:218 , THR B:238 , ILE B:239 , HOH B:471binding site for residue CL B 303
7AC7SOFTWAREPHE A:199 , LYS A:224 , LEU A:225 , ARG A:226 , THR A:228 , HIS A:230 , HOH A:414 , HOH A:415 , SER C:48 , GLY C:49 , THR C:50 , GLY C:51 , LYS C:52 , THR C:53 , LEU C:54 , SER C:89 , PHE C:90 , ARG C:218 , ILE C:239 , THR C:240 , ASP C:241 , MG C:302 , HOH C:405 , HOH C:412 , HOH C:414 , HOH C:421 , HOH C:434binding site for residue ANP C 301
8AC8SOFTWARETHR C:53 , ANP C:301 , HOH C:405 , HOH C:414 , HOH C:434binding site for residue MG C 302
9AC9SOFTWAREARG C:218 , THR C:238 , ILE C:239binding site for residue CL C 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TL6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:145 -Ser A:146
2Asp B:145 -Ser B:146
3Asp C:145 -Ser C:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TL6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TL6)

(-) Exons   (0, 0)

(no "Exon" information available for 4TL6)

(-) 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tl6 A  15 HQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAM 252
                                    24        34        44        54        64        74        84        94       104       122       132       142   ||  160       170       180       190       200       210       220       230       240       250  
                                                                                                                           112|                      146|                                                                                                 
                                                                                                                            121                       155                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee......hhhhhhhhhhhhhhhh..eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeee...................eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl6 B  17 AIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 249
                                    26        36        46        56        66        76        86        96       106   ||  125       135       145       155       165       175       185       195       205       215       225       235       245    
                                                                                                                       110|                                                                                                                                 
                                                                                                                        120                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl6 C  16 QAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAM 252
                                    25        35        45        55        65        75        85        95       105       123       133       143  ||   161       171       181       191       201       211       221       231       241       251 
                                                                                                                           113|                     146|                                                                                                 
                                                                                                                            122                      155
   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 4TL6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TL6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TL6)

(-) Gene Ontology  (21, 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
    Asp A:145 - Ser A:146   [ RasMol ]  
    Asp B:145 - Ser B:146   [ RasMol ]  
    Asp C:145 - Ser C:146   [ 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
  4tl6
    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
  KAIC_SYNE7 | Q79PF4
    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
  KAIC_SYNE7 | Q79PF4
    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
        KAIC_SYNE7 | Q79PF4: 1tf7 1u9i 2gbl 3dvl 3jzm 3k09 3k0a 3k0c 3k0e 3k0f 3s1a 4dug 4ijm 4tl7 4tl8 4tl9 4tla 4tlb 4tlc 4tld 4tle 5c5e 5n8y

(-) Related Entries Specified in the PDB File

4tl7 4tl8 4tl9 4tla 4tlb 4tlc 4tld 4tle