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(-) Description

Title :  STRUCTURE OF THE FHA1 DOMAIN OF RAD53 BOUND SIMULTANEOUSLY TO THE BRCT DOMAIN OF DBF4 AND A PHOSPHOPEPTIDE.
 
Authors :  A. Guarne, A. Almawi, L. Matthews
Date :  24 Aug 16  (Deposition) - 12 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Fha; Brct; Phosphopeptide; 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
    Chains: A, C
    EC Number: 2.7.12.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP P32325 RESIDUES 105-220 LINKED TO UNP P22216 RESIDUES 22-162 VIA LINKER RESIDUES VDGS
    Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DUMBBELL FORMING PROTEIN 4,CHEK2 HOMOLOG,SERINE-PROTEIN KINASE 1
 
Molecule 2 - ASP-GLY-GLU-SER-TPO-ASP-GLU-ASP-ASP
    Chains: B, D
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: SHORT PHOSPHORYLATED PEPTIDE DERIVED FROM CDC7
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (2, 13)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:109 , HOH A:519 , THR C:242binding site for residue GOL A 401
02AC2SOFTWAREARG A:238binding site for residue GOL A 402
03AC3SOFTWARETRP A:202 , LYS A:206 , ASN C:315 , GLU C:332 , HOH C:535binding site for residue GOL C 401
04AC4SOFTWAREASN A:315 , GLU A:332 , LYS C:200 , TRP C:202 , LYS C:206binding site for residue GOL C 402
05AC5SOFTWARETRP C:112 , HOH C:502 , HOH C:546binding site for residue GOL C 403
06AC6SOFTWAREGLN C:245 , ARG C:249 , HIS C:280 , GLY C:282binding site for residue GOL C 404
07AC7SOFTWAREARG C:238 , PHE C:349 , ILE C:350 , ASN C:351 , HOH C:563binding site for residue GOL C 405
08AC8SOFTWAREASN C:289 , LYS C:290 , GOL D:101binding site for residue GOL C 406
09AC9SOFTWAREVAL C:337 , GLY C:338binding site for residue GOL C 407
10AD1SOFTWAREILE C:248 , ARG C:249binding site for residue GOL C 408
11AD2SOFTWAREGOL C:406 , HOH D:205binding site for residue GOL D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T2S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T2S)

(-) Exons   (0, 0)

(no "Exon" information available for 5T2S)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhhhhh..ee.........eee......hhhhh...hhhhhhhhh..eeehhhhhhhhhhhh......eeeeeeee.......eeeeehhhhhhhh.....eeeeee......ee...........eeeee.....eeeee......ee..ee......ee....eeeee........eeeeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2s A 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDIGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQNK 362
                                   112       122       132       142       152       162       172       182       192       202       212    || 235       245       255       265       275       285       295       305       315       325       335       345       355       
                                                                                                                                            217|                                                                                                                                   
                                                                                                                                             231                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5t2s B   1 DGEStDEDD   9
                                |    
                                5-TPO


Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               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....eeeee.....eee..ee......ee......eee........eeeeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2s C 103 HMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPACDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVGVGVESDILSLVIFINDKFKQCLEQ 360
                                   112       122       132       142       152       162       172       182       192       202       212       233       243       253       263       273       283       293       303       313       323       333       343       353       
                                                                                                                                               220|                                                                                                                                
                                                                                                                                                232                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5t2s D   1 DGEStDEDD   9
                                |    
                                5-TPO
   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 5T2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T2S)

(-) Gene Ontology  (48, 73)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DBF4_YEAST | P32325: 3oq0 3oq4 3qbz 5t2f
        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 5t2f

(-) Related Entries Specified in the PDB File

5t2f TWO STRUCTURES WERE SOLVED ON THIS WORK. THE BINARY COMPLEX IS ENTRY 5T2F AND THE TERNARY COMPLEX (WITH A PHOSPHOPEPTIDE) IS THIS ENTRY.