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 BINARY COMPLEX BUD32-CGI121 IN COMPLEX WITH ADP
 
Authors :  W. Zhang, H. Van Tilbeurgh
Date :  10 Nov 14  (Deposition) - 18 Mar 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Keops, Binary Complex, Bud32-Cgi121, Trna T6A, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhang, B. Collinet, M. Graille, M. C. Daugeron, N. Lazar, D. Libri, D. Durand, H. Van Tilbeurgh
Crystal Structures Of The Gon7/Pcc1 And Bud32/Cgi121 Complexes Provide A Model For The Complete Yeast Keops Complex.
Nucleic Acids Res. V. 43 3358 2015
PubMed-ID: 25735745  |  Reference-DOI: 10.1093/NAR/GKV155

(-) Compounds

Molecule 1 - EKC/KEOPS COMPLEX SUBUNIT BUD32
    Chains: A
    EC Number: 3.6.-.-, 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: BUD32, LDB14, YGR262C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ATYPICAL SERINE/THREONINE PROTEIN KINASE BUD32,BUD SITE SELECTION PROTEIN 32,LOW-DYE-BINDING PROTEIN 14,PID261,BUD32
 
Molecule 2 - EKC/KEOPS COMPLEX SUBUNIT CGI121
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: CGI121, YML036W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: CGI-121 HOMOLOG,CGI121

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:52 , ASP A:182 , ADP A:302binding site for residue MG A 301
2AC2SOFTWARESER A:23 , ILE A:50 , LYS A:52 , GLU A:107 , LEU A:109 , ASP A:182 , MG A:301 , HOH A:431 , HOH A:456 , HOH A:510 , HOH A:549binding site for residue ADP A 302
3AC3SOFTWAREARG A:143 , LYS A:216 , TRP A:220 , GLU A:223 , MET A:259binding site for residue SO4 A 303
4AC4SOFTWAREPHE A:125 , HIS A:129 , LEU A:137 , TRP A:176binding site for residue SO4 A 304
5AC5SOFTWARESER A:135 , ASP A:136 , ARG A:253 , ARG A:257 , HOH A:416binding site for residue SO4 A 305
6AC6SOFTWARELEU A:199 , LEU A:202 , GLU A:203 , ASN A:218 , ILE A:221 , HOH A:527binding site for residue ACT A 306
7AC7SOFTWARELEU A:191 , VAL A:192 , GLU A:193 , ARG A:246binding site for residue ACT A 307
8AC8SOFTWARELYS B:68 , ILE B:134 , GLU B:135 , ASN B:140 , HOH B:303 , HOH B:399binding site for residue SO4 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WW9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WW9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WW9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WW9)

(-) Exons   (0, 0)

(no "Exon" information available for 4WW9)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.....eeee...eeeee...............eeeee...hhhhhhhhhhhhh........eeeee....eeeee....eehhhhee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.ee........eeeeee..eeeeee......ee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ww9 A   4 EFIDKVSSYLTPDVDIAPISQGAIVFTTTTHPYLPRAKDSHQKYIIKYRPRTLNESRLLAKLYLIPGLCVPQLIACDPYNGFIWLEFLGEDLPGGHGFSNLKNFLWMHDQDPYSDLVATTLRKVGRQIGLLHWNDYCHGDLTSSNIVLVRDGARWTPHLIDFGLGSVSNLVEDKGVDLYVLERAILSTHSKHAEKYNAWIMEGFEEVYREQGAKGAKKLKEVTKRFEEVRLRGRKRSM 259
                                    13        23 ||     35        45        55|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        
                                                25|                         55|                                                                                                                                                                                           
                                                 28                          72                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeee...hhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhh.......eeeeeee......hhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ww9 B   1 MVVSIIPQFPDIKVSLALFEQVKNAKEIRSKMSELSFAFIDPRLVCSGEQMYSAIYKTLIEVKYNKMRTRNLNSECVLCLSPTSNISDAFLKFGIKDDSSQLICLKFHTNTDDVDKEQLRTIMTSIVKGQEIEFNDDNLSRFYDEALIRKIYKLSDDFKPQDVNGLSRALVDAIQLR 179
                                    10        20        30    ||  42        52        62        72        82        92       102       112       122       132       142       152       162       172       
                                                             35|                                                                                                                                             
                                                              38
   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 4WW9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WW9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WW9)

(-) Gene Ontology  (31, 44)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ww9)
 

(-) 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
  4ww9
    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
  BUD32_YEAST | P53323
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CG121_YEAST | Q03705
    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
  3.6.-.-
    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
  BUD32_YEAST | P53323
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CG121_YEAST | Q03705
    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
        BUD32_YEAST | P53323: 4ww5 4ww7 4wwa
        CG121_YEAST | Q03705: 4ww5 4ww7 4wwa 4xah

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WW9)