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(-) Description

Title :  CRYSTAL STRUCTURE OF RAD53 KINASE DOMAIN AND SCD2 IN COMPLEX WITH AMPPNP
 
Authors :  C. S. Ho, L. E. Wybenga-Groot, D. F. Ceccarelli, F. Sicheri
Date :  21 Apr 14  (Deposition) - 28 May 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Kinase Domain, Anp, 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 Plasmid: PPROEX-HTA-TEV
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:212 , SER A:225 , MET A:273 , GLU A:274 , VAL A:276 , ASP A:280 , ASP A:323 , ASN A:324 , LEU A:326binding site for residue ANP A 601
2AC2SOFTWARESER B:225 , MET B:273 , GLU B:274 , VAL B:276 , ASP B:280 , ASP B:323 , ASN B:324 , LEU B:326binding site for residue ANP B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr B:191 -Gly B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PDS)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeee....eeeeee.....eeeeeee..hhhhhhhhh.......eeeee..eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........eeeee....eeee...........hhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.....ee....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pds A 191 TGIFKDFSIIDEVTVKKAIERTTGKTFSVKIIVTRELEVLQKLNHPRIVRLKGFYESYYMVMEFVSGGDLMDFVAAHGAVGEDAGREISRQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITAFGLAKVAYVAPEVIRRNEYSSLVDMWSMGCLVYVILTGHLPFSGSTQDQLYKQIGRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPWIKMSPLSYGDFSQISLSQSLSQ 490
                                   200  ||   217       227 ||    248       258    || 271       281       291       301       311       321       331       341   ||  365  ||   388       398       408       418       428       438       448       458       468  ||   481         
                                      203|               229|                   263|                                                                           345|     368|                                                                                      471|               
                                       211                241                    267                                                                            360      382                                                                                       475               


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheee..eeeeeee.....eeeeee...hhhhhhhhh.......eeee..eeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........eeeee....eeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pds B 191 TGIFKDFSIIATVKKAIERTTGKTFSVKIIVTRELEVLQKLNHPRIVRLKGFYYYMVMEFVSGGDLMDFVAAHGAVGEDAGREISRQILTAIKYIHSMGISHRDLKPDNILIEQDDPVLVKITAFGLAKVTLAYVAPEVINEYSSLVDMWSMGCLVYVILTGHLPFSGSTQDQLYKQIGRGSYHEGPLKDFRISEEARDFIDSLLQVDPNNRSTAAKALNHPWIKMSPLYGDFSQISLSQSLSQQKLL 494
                                   200|      219       229|      250       260  ||   275       285       295       305       315       325       335       345|      367|      392       402       412       422       432       442       452       462       476       486        
                                   200|                229|                   263|                                                                         345|      367|                                                                                     471|                  
                                    210                 241                    269                                                                          358       383                                                                                      476
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  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 4PDS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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  RAD53_YEAST | P22216
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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 4pdp 5t2f 5t2s

(-) Related Entries Specified in the PDB File

4pdp RAD53 KINASE DOMAIN AND SCD2 IN APO FORM AT HIGHER RESOLUTION