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(-) Description

Title :  HE CATALYTIC CORE OF RAD2 IN COMPLEX WITH DNA SUBSTRATE (COMPLEX II)
 
Authors :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, M. Nowotny
Date :  02 Apr 14  (Deposition) - 27 Aug 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ba Rossmann-Like, Dna Repair, Tfiih, Nucleus, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, J. Studnicka, M. Nowotny
Crystal Structure Of The Catalytic Core Of Rad2: Insights Into The Mechanism Of Substrate Binding.
Nucleic Acids Res. V. 42 10762 2014
PubMed-ID: 25120270  |  Reference-DOI: 10.1093/NAR/GKU729

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD2
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) ROSSETA
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: RAD2
    Gene: RAD2, YGR258C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - DNA (5'- D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2K2Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:792 , GLU A:794 , ASP A:813 , ASP A:815 , ASP A:864 , HOH A:1144 , HOH A:1267BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWARELEU A:869 , MET A:872 , HOH A:1109 , HOH A:1130 , HOH A:1198 , DC D:9BINDING SITE FOR RESIDUE K A 1002
3AC3SOFTWAREGLU B:794 , ASP B:813 , ASP B:815 , ASP B:864 , HOH B:1296BINDING SITE FOR RESIDUE CA B 1001
4AC4SOFTWARELEU B:860 , LEU B:869 , MET B:872 , HOH B:1209 , HOH B:1297 , HOH C:118BINDING SITE FOR RESIDUE K B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q0W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:929 -Pro A:930
2Phe B:929 -Pro B:930

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q0W)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q0W)

(-) 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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeee.hhhh..eeeee..hhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh...eeee.......eeeeeehhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0w A   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDQNAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKERRQGKREDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41   ||   53        63        73        83        93      |767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977      
                                                                      45|                                                 100|                                                                                                                                                                                                                          
                                                                       48                                                  765                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeee.hhhh..eeeee..hhhhhh...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh....eee.......eeeeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0w B   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKEKRDSDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLIRD 985
                                    11        21        31       |51        61        71        81        91 ||    768       778       788       798       808       818       828       838       848       858       868       878       888       898|      914       924       934       944       954       964       974       984 
                                                                39|                                         93|                                                                                                                                      898|                                                                                
                                                                 50                                         761                                                                                                                                       905                                                                                


Chain C from PDB  Type:DNA  Length:16
                                                
                 4q0w C   1 TGATCCGTCCACCTTT  16
                                    10      


Chain D from PDB  Type:DNA  Length:15
                                               
                 4q0w D   1 TAGGTGGACGGATCA  15
                                    10
   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 4Q0W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q0W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q0W)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Phe A:929 - Pro A:930   [ RasMol ]  
    Phe B:929 - Pro B:930   [ RasMol ]  
 

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  4q0w
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  RAD2_YEAST | P07276
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD2_YEAST | P07276: 2lox 4q0r 4q0z 4q10

(-) Related Entries Specified in the PDB File

4q0r 4q0z 4q10