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(-) Description

Title :  STRUCTURE OF THE FHA1 DOMAIN OF RAD53 BOUND TO THE BRCT DOMAIN OF DBF4
 
Authors :  A. Guarne, A. W. Almawi, L. A. Matthews
Date :  23 Aug 16  (Deposition) - 15 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Fha; Brct; Protein Chimera, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. W. Almawi, L. A. Matthews, P. Myrox, S. Boulton, C. Lai, T. Moraes, G. Melacini, R. Ghirlando, B. P. Duncker, A. Guarne
'And' Logic Gates At Work: Crystal Structure Of Rad53 Bound To Dbf4 And Cdc7.
Sci Rep V. 6 34237 2016
PubMed-ID: 27681475  |  Reference-DOI: 10.1038/SREP34237

(-) Compounds

Molecule 1 - DDK KINASE REGULATORY SUBUNIT DBF4,SERINE/THREONINE-PROTEIN KINASE RAD53 CHIMERIC PROTEIN
    22-161 Via Linker Residues: VDSGASGGS
    Chains: A, B, C, D
    EC Number: 2.7.12.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP P32325 RESIDUES 105-220 LINKED TO UNP P22216 RESIDUES
    Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE, SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DUMBBELL FORMING PROTEIN 4,CHEK2 HOMOLOG,SERINE-PROTEIN KINASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:195 , LYS A:200 , VAL A:201 , TRP A:202 , LYS A:206 , ASN D:320 , GLU D:337binding site for residue EDO A 401
02AC2SOFTWAREMET A:104 , LEU A:109 , TRP A:112 , ASN A:213 , HOH A:518binding site for residue EDO A 402
03AC3SOFTWARETHR A:247 , GLU A:337 , VAL A:352 , TRP D:112 , TRP D:116 , EDO D:404binding site for residue EDO A 403
04AC4SOFTWARETYR B:183 , LYS B:196 , HOH B:515 , GLN C:322binding site for residue EDO B 401
05AC5SOFTWARELEU B:109 , TRP B:112 , THR C:247binding site for residue EDO B 403
06AC6SOFTWARESER C:290 , SER C:293 , THR C:314 , HOH C:1137binding site for residue EDO C 1001
07AC7SOFTWARELEU C:109 , ASN C:213 , EDO C:1003binding site for residue EDO C 1002
08AC8SOFTWARETRP C:112 , LYS C:206 , ARG C:209 , PHE C:210 , ASN C:213 , EDO C:1002binding site for residue EDO C 1003
09AC9SOFTWAREARG D:243binding site for residue EDO D 401
10AD1SOFTWARETHR D:188 , ASP D:189 , GLU D:325 , SER D:328 , HOH D:514binding site for residue EDO D 402
11AD2SOFTWAREEDO A:403 , LEU D:109 , ASN D:213binding site for residue EDO D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T2F)

(-) Exons   (0, 0)

(no "Exon" information available for 5T2F)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhhhhh..eee........eeee..hhhhhhhh...hhhhhhhhh..eeeehhhhhhhhhh....eeeeeeee.......eeeeehhhhhhhh...eeeeeeee......ee...........eeeeee....eeeee......ee..ee......ee......eee........eeeeeeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2f A 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMYKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCL 363
                                   112       122       132   ||| 145       155       165       175       185       195       205       215||     246       256       266       276       286       296       306       316       326       336       346       356       
                                                           136||                                                                        216|                                                                                                                             
                                                            139|                                                                         238                                                                                                                             
                                                             141                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhheeee........hhhhhhhhhhhhhhhhhhhhhh..eee........eee......hhhhh...hhhhhhhhh..eeehhhhhhhhhhhh.....eeeeeeee.......eeeeehhhhhhhh.....eeeeee......ee...........eeeee.hhh.eeeee......ee..ee......ee......eee........eeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2f B 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVIGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQ 365
                                   112       122       132       142       152       162       172       182       192       202       212   ||  241       251       261       271       281       291       301       311       321       331       341       351       361    
                                                                                                                                           216|                                                                                                                                 
                                                                                                                                            236                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhhhhh..eee........eeee.....hhhhh...hhhhhhhhh..eeeehhhhhhhhhhh.......eeeeeeee.......eeeeehhhhhhhh...eeeeeeee......ee...........eeeeee...eeeeee......ee..ee.....eee......eee........eeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2f C 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQNK 367
                                   112       122       132       142       152       162       172       182       192       202       212      |239       249       259       269       279       289       299       309       319       329       339       349       359        
                                                                                                                                              219|                                                                                                                                  
                                                                                                                                               237                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhh..ee.........eeee..hhhhh......hhhhhhhhh..eeeehhhhhhhhhh.......eeeeeeee.......eeeeehhhhhhhh.....eeeeee......ee...........eeeee.hhh.eeeee.....eee..ee......ee.....eeee...hhhhheeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2f D 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVNYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQNK 367
                                   112       122       132 |||   145       155       165       175       185       195       205       215  ||   243       253       263       273       283       293       303       313       323       333       343       353       363    
                                                         134||                                                                            218|                                                                                                                                  
                                                          137|                                                                             237                                                                                                                                  
                                                           139
   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 5T2F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T2F)

(-) Gene Ontology  (40, 45)

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  RAD53_YEAST | P22216
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  2.7.12.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        DBF4_YEAST | P32325: 3oq0 3oq4 3qbz 5t2s
        RAD53_YEAST | P22216: 1dmz 1fhq 1fhr 1g3g 1g6g 1j4k 1j4l 1j4o 1j4p 1j4q 1k2m 1k2n 1k3j 1k3n 1k3q 1qu5 2a0t 2jqi 2jql 2ygv 4pdp 4pds 5t2s

(-) Related Entries Specified in the PDB File

5t2s