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(-) Description

Title :  HUMAN CDC7 KINASE IN COMPLEX WITH DBF4 AND PHA767491
 
Authors :  S. Hughes, P. Cherepanov
Date :  18 May 12  (Deposition) - 31 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ser/Thr Protein Kinase, Transferase, Phosphorylation, Cell Cycle, Cell Division, Mitosis, S Phase, Serine/Threonine-Protein Kinase, Dbf4-Dependent Kinase, Ddk, Atp-Binding, Nucleotide-Binding, Zinc- Binding, Nucleus, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Hughes, F. Elustondo, A. Di Fonzo, F. G. Leroux, A. C. Wong, A. P. Snijders, S. J. Matthews, P. Cherepanov
Crystal Structure Of Human Cdc7 Kinase In Complex With Its Activator Dbf4.
Nat. Struct. Mol. Biol. V. 19 1101 2012
PubMed-ID: 23064647  |  Reference-DOI: 10.1038/NSMB.2404

(-) Compounds

Molecule 1 - CELL DIVISION CYCLE 7-RELATED PROTEIN KINASE
    ChainsA, C
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSF-DUET
    Expression System StrainROSETTA-2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCDC7, CDC7L1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC7-RELATED KINASE, HSCDC7, HUCDC7
 
Molecule 2 - PROTEIN DBF4 HOMOLOG A
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDF-DUET
    Expression System StrainROSETTA-2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneASK, DBF4, DBF4A, ZDBF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymACTIVATOR OF S PHASE KINASE, CHIFFON HOMOLOG A, DBF4-TYPE ZINC FINGER-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
10SY2Ligand/Ion2-(PYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10SY1Ligand/Ion2-(PYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10SY1Ligand/Ion2-(PYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:88 , LYS A:90 , PRO A:135 , TYR A:136 , LEU A:137 , LEU A:184 , VAL A:195 , ASP A:196 , HOH A:715BINDING SITE FOR RESIDUE 0SY A 601
2AC2SOFTWARECYS B:296 , CYS B:299 , HIS B:309 , HIS B:315BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWAREVAL C:72 , ALA C:88 , LYS C:90 , MET C:118 , PRO C:135 , LEU C:137 , VAL C:195 , ASP C:196 , HOH C:715BINDING SITE FOR RESIDUE 0SY C 601
4AC4SOFTWARECYS D:296 , CYS D:299 , HIS D:309 , HIS D:315BINDING SITE FOR RESIDUE ZN D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F9B)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:412 -Pro A:413
2Lys A:570 -Asp A:571
3Lys B:217 -Pro B:218
4Lys B:248 -Pro B:249
5Tyr C:412 -Pro C:413
6Lys C:570 -Asp C:571
7Lys D:217 -Pro D:218
8Lys D:248 -Pro D:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F9B)

(-) Exons   (0, 0)

(no "Exon" information available for 4F9B)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh..........eeeee..eeeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee.....hhhhhhh............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f9b A  39 GVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQSEAQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDM 572
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218 ||    377       387       397       407       417       427       437       447       457       534       544       554       564        
                                                                                                                                                                                                               220|                                                                                             466|                                      
                                                                                                                                                                                                                370                                                                                              534                                      

Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......eeee....................ee....ee..hhhhhhhhhhhhhhhhh..hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4f9b B 214 RLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYE 342
                                   223       233       243       253||     302       312       322       332       342
                                                                  254|                                                
                                                                   294                                                

Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh..........eeeee..eeeeeee.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee.hhhhhee.....hhhhhhh........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9b C  37 LAGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQSEAQRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDM 572
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  ||   379       389       399       409       419       429       439       449       459      |536       546       556       566      
                                                                                                                                                                                                                219|                                                                                          466|                                      
                                                                                                                                                                                                                 373                                                                                           534                                      

Chain D from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......eeee..............................hhhhhhhhhhhhhhhhh..hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4f9b D 214 RLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYE 342
                                   223       233       243       253||     302       312       322       332       342
                                                                  254|                                                
                                                                   294                                                

   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 4F9B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F9B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F9B)

(-) Gene Ontology  (32, 38)

Asymmetric Unit(hide GO term definitions)

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    Tyr A:412 - Pro A:413   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC7_HUMAN | O003114f99 4f9a 4f9c 5uwq 5uwr
        DBF4A_HUMAN | Q9UBU74f99 4f9a 4f9c

(-) Related Entries Specified in the PDB File

4f99 4f9a 4f9c