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 PHO85-PCL10-ATP-GAMMA-S COMPLEX
 
Authors :  F. A. Quiocho, F. Zheng
Date :  16 May 13  (Deposition) - 18 Sep 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycogen Synthesis, Glycogen Synthesis Regulation, Transferase- Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zheng, F. A. Quiocho
New Structural Insights Into Phosphorylation-Free Mechanism For Full Cyclin-Dependent Kinase (Cdk)-Cyclin Activity And Substrate Recognition.
J. Biol. Chem. V. 288 30682 2013
PubMed-ID: 24022486  |  Reference-DOI: 10.1074/JBC.M113.502773

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT PROTEIN KINASE PHO85
    Chains: A
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: P7102.18A, PHO85, SSG3, YPL031C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: NEGATIVE REGULATOR OF THE PHO SYSTEM, SERINE/THREONINE- PROTEIN KINASE PHO85
 
Molecule 2 - PHO85 CYCLIN-10
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSBET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 227-433
    Gene: G2838, PCL10, YGL134W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AGS1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:138 , ASP A:151 , AGS A:402BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREGLY A:16 , THR A:17 , TYR A:18 , VAL A:21 , ALA A:34 , LYS A:36 , GLU A:83 , MET A:85 , ASP A:88 , ASP A:133 , LYS A:135 , GLN A:137 , ASN A:138 , LEU A:140 , ASP A:151 , MG A:401 , HOH A:504BINDING SITE FOR RESIDUE AGS A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:102 -Arg A:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KRC)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4krca_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeeee...eeeeeeee.....eeeeeeee.......hhhhhhhhhh...........eeeeeee..eeeeeee...eehhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh......hhhhhhh.............hhhhhhhhhh....hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krc A   2 SSSSQFKQLEKLGNGTYATVYKGLNKTTGVYVALKEVKLDSEEGTPSTAIREISLMKELKHENIVRLYDVIHTENKLTLVFEFMDNDLKKYMDSRTPRGLELNLVKYFQWQLLQGLAFCHENKILHRDLKPQNLLINKRGQLKLGDFGLARAFGIPVNTFSSEVVTLWYRAPDVLMGSRTYSTSIDIWSCGCILAEMITGKPLFPGTNDEEQLKLIFDIMGTPNESLWPSVTKLPKYNPNIQQRPPRDLRQVLQPHTKEPLDGNLMDFLHGLLQLNPDMRLSAKQALHHPWFAEYYH 302
                                    11        21        31        41        51        61        71        81        91     ||105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       
                                                                                                                          97|                                                                                                                                                                                                        
                                                                                                                          102                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheee.....eee....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4krc B 244 ENPLLHGIPVDVPHISVDEALANFKETIELLLKLSGNNTRVEKKEYSNFYMKSKPTLSSADFLKRIQDKCEYQPTVYLVATFLIDTLFLTRDGNNILQLKLNLQEKEVHRMIIAAVRLSTKLLEDFVHSHEYFSKVCGISKRLLTKLEVSLLICVCNTKLMVSNRKLAASKLLLNELRSF 431
                                   253 ||    265       275      |291       301       311       321       331       341       351       361       371       381       391       401       411       421       431
                                     255|                     282|                                                                                                                                              
                                      258                      289
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 36)

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
    AGS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:102 - Arg A:103   [ 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 | 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
  4krc
    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
  PCL10_YEAST | P53124
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PHO85_YEAST | P17157
    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)
  2.7.11.22
    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
  PCL10_YEAST | P53124
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PHO85_YEAST | P17157
    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
        PCL10_YEAST | P53124: 4krd
        PHO85_YEAST | P17157: 2pk9 2pmi 4krd

(-) Related Entries Specified in the PDB File

4krd