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(-) Description

Title :  HUMAN CDC7 KINASE IN COMPLEX WITH DBF4 AND XL413
 
Authors :  S. Hughes, P. Cherepanov
Date :  18 May 12  (Deposition) - 31 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B
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
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF-DUET
    Expression System Strain: ROSETTA-2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDC7, CDC7L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDC7-RELATED KINASE, HSCDC7, HUCDC7
 
Molecule 2 - PROTEIN DBF4 HOMOLOG A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDF-DUET
    Expression System Strain: ROSETTA-2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ASK, DBF4, DBF4A, ZDBF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACTIVATOR OF S PHASE KINASE, CHIFFON HOMOLOG A, DBF4-TYPE ZINC FINGER-CONTAINING PROTEIN 1

 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
10SX1Ligand/Ion8-CHLORO-2-[(2S)-PYRROLIDIN-2-YL][1]BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , VAL A:72 , ALA A:88 , LYS A:90 , MET A:118 , MET A:134 , PRO A:135 , TYR A:136 , LEU A:137 , ASN A:182 , LEU A:184 , VAL A:195 , ASP A:196 , HOH A:731 , HOH A:766BINDING SITE FOR RESIDUE 0SX A 601
2AC2SOFTWARECYS B:296 , CYS B:299 , HIS B:309 , HIS B:315BINDING SITE FOR RESIDUE ZN B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F9C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F9C)

(-) Exons   (0, 0)

(no "Exon" information available for 4F9C)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeeeee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh..........eeeee..eeeeeee.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee.....hhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f9c A  41 KKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDM 572
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   ||  378       388       398       408       418       428       438       448       458       536       546       556       566      
                                                                                                                                                                                                       214|                                                                                          466|                                     
                                                                                                                                                                                                        373                                                                                           535                                     


Chain B from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....eeee....................ee....ee..hhhhhhhhhhhhhhhh...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4f9c B 214 RLKKPFVKVEDMSQRPFYLQLTNMPFINYSIQKPCSPFDGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYE 342
                                   223   ||  235       245       294       304       314       324       334        
                                       227|                     254|                                                
                                        230                      294
   Legend:   → Mismatch (orange background)
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  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 4F9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F9C)

(-) Gene Ontology  (32, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:570 - Asp A:571   [ RasMol ]  
    Lys B:217 - Pro B:218   [ RasMol ]  
    Lys B:248 - Pro B:249   [ RasMol ]  
    Tyr A:412 - Pro A:413   [ RasMol ]  
 

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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC7_HUMAN | O00311: 4f99 4f9a 4f9b 5uwq 5uwr
        DBF4A_HUMAN | Q9UBU7: 4f99 4f9a 4f9b

(-) Related Entries Specified in the PDB File

4f99 4f9a 4f9b