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(-) Description

Title :  CRYSTAL STRUCTURE OF RAD53 KINASE DOMAIN AND SCD2
 
Authors :  L. E. Wybenga-Groot, C. S. Ho, D. F. Ceccarelli, F. Sicheri
Date :  19 Apr 14  (Deposition) - 28 May 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Ser/Thr Kinase Domain, N-Lobe, C-Lobe, Activation Segment Exchange, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Wybenga-Groot, C. S. Ho, F. D. Sweeney, D. F. Ceccarelli, C. J. Mcglade, D. Durocher, F. Sicheri
Structural Basis Of Rad53 Kinase Activation By Dimerization And Activation Segment Exchange.
Cell Signal. V. 26 1825 2014
PubMed-ID: 24815189  |  Reference-DOI: 10.1016/J.CELLSIG.2014.05.004

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE RAD53
    Chains: A, B
    EC Number: 2.7.12.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: KINASE DOMAIN AND SCD2 (UNP RESIDUES 170-512)
    Gene: RAD53, MEC2, SAD1, SPK1, YPL153C, P2588
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CHEK2 HOMOLOG,SERINE-PROTEIN KINASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4PDP)

(-) Sites  (0, 0)

(no "Site" information available for 4PDP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr B:191 -Gly B:192
2Val B:204 -Gly B:205
3Asp B:331 -Pro B:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PDP)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeee.eeeeeee.....eeeeeee......hhhhhhhhhh.........eeeee...eeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee....eeee......ee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhh..........ee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdp A 191 TGIFKDFSIIATVKKAIERTTGKTFSVKIISKRKMDGVTRELEVLQKLNHPRIVRLKGFYEDSYYMVMEFVSGGDLMDFVAAHGAVGEDAGREISRQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITAFGLAKVQTLAYVAPEVIRRNEYSSLVDMWSMGCLVYVILTGHLPFSGSTQDQLYKQIGRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPWIKMSPLYGDFSQISLSQSLSQQKLL 494
                                   200|      219       229   ||  243       253       263 ||    275       285       295       305       315       325       335       345||     366 ||    389       399       409       419       429       439       449       459       469 ||    483       493 
                                   200|                    233|                        265|                                                                           346|       368|                                                                                      471|                  
                                    210                     238                         268                                                                            358        382                                                                                       476                  


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeee.......eeeeeee.....eeeeee....hhhhhhhhhh.........eeeee....eeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee....eeee......ee.hhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhh..hhhhh.hhhhhh..................hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdp B 191 TGIFKDFSIIDEVVGQATVKKAIERTTGKTFSVKIISKDGVTRELEVLQKLNHPRIVRLKGFYEDSYYMVMEFVSGGDLMDFVAAHGAVGEDAGREISRQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITAFGLAKVQTLAYVAPEVINEYSSLVDMWSMGCLVYVILTGHLPFSGSTQDQLYKQIGRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPWIKMSPLSYGDFSQISLSQSLSQQKLLEN 496
                                   200     ||213       223       240       250       260    || 272       282       292       302       312       322       332       342   ||  363   ||  388       398       408       418       428       438       448       458       468  ||   481       491     
                                         206|                  231|                       265|                                                                           346|      367|                                                                                     471|                     
                                          210                   239                        268                                                                            358       383                                                                                      475
   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 4PDP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

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  Cis Peptide Bonds
    Asp B:331 - Pro B:332   [ RasMol ]  
    Thr B:191 - Gly B:192   [ RasMol ]  
    Val B:204 - Gly B:205   [ RasMol ]  
 
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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
        RAD53_YEAST | P22216: 1dmz 1fhq 1fhr 1g3g 1g6g 1j4k 1j4l 1j4o 1j4p 1j4q 1k2m 1k2n 1k3j 1k3n 1k3q 1qu5 2a0t 2jqi 2jql 2ygv 4pds 5t2f 5t2s

(-) Related Entries Specified in the PDB File

4pds