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(-) Description

Title :  MRE11 RAD50 BINDING DOMAIN BOUND TO RAD50
 
Authors :  G. J. Williams, R. S. Williams, A. Arvai, G. Moncalian, J. A. Tainer
Date :  01 Feb 11  (Deposition) - 30 Mar 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Reca-Like Fold, Coiled-Coils, Atpase, Exonuclease, Endonuclease, Atp Binding, Dna Binding, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. J. Williams, R. S. Williams, J. S. Williams, G. Moncalian, A. S. Arvai, O. Limbo, G. Guenther, S. Sildas, M. Hammel, P. Russell, J. A. Tainer
Abc Atpase Signature Helices In Rad50 Link Nucleotide State To Mre11 Interface For Dna Repair.
Nat. Struct. Mol. Biol. V. 18 423 2011
PubMed-ID: 21441914  |  Reference-DOI: 10.1038/NSMB.2038

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    ChainsA
    EC Number3.6.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN (UNP RESIDUES 1-195)
    GeneRAD50, PF1167
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    SynonymRAD50 ABC-ATPASE
 
Molecule 2 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    ChainsB
    EC Number3.6.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL DOMAIN (UNP RESIDUES 704-882)
    GeneRAD50, PF1167
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    SynonymRAD50 ABC-ATPASE
 
Molecule 3 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    ChainsC
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRAD50 BINDING DOMAIN (UNP RESIDUES 348-381)
    GeneMRE11, PF1166
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    SynonymMRE11 NUCLEASE, PFMRE11

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:33 , SER A:34 , GLY A:35 , LYS A:36 , SER A:37BINDING SITE FOR RESIDUE PO4 A 200
2AC2SOFTWAREARG A:83BINDING SITE FOR RESIDUE PO4 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QKR)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:49 -Pro A:50
2Gly A:196 -Gly A:197
3Glu B:823 -Pro B:824

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QKR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QKR)

(-) Exons   (0, 0)

(no "Exon" information available for 3QKR)

(-) 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:199
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
          RAD50_PYRFU     1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTENIEE 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----AAA_23-3qkrA01 A:5-195                                                                                                                                                                         ---- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.........hhhhhh....eeeeeeee....eeeeeeee........eeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qkr A   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTEGGHH 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:179
                                   713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873         
          RAD50_PYRFU   704 AEKENRERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains AAA_21-3qkrB01 B:704-861                                                                                                                                      --------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee....eee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh..eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qkr B 704 AEKENRERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                   713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873         

Chain C from PDB  Type:PROTEIN  Length:32
 aligned with MRE11_PYRFU | Q8U1N9 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:32
                                   357       367       377  
          MRE11_PYRFU   348 SDFFTEFELKIIDILGEKDFDDFDYIIKLITE 379
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 3qkr C 348 SDFFTEFELKIIDILGEKDFDDFDYIIKLITE 379
                                   357       367       377  

   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 3QKR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QKR)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (16, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RAD50_PYRFU | P58301)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

Chain C   (MRE11_PYRFU | Q8U1N9)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MRE11_PYRFU | Q8U1N91ii7 1s8e 3dsc 3dsd 3qks 3qku 4hd0
        RAD50_PYRFU | P583011f2t 1f2u 1ii8 1l8d 1us8 3qks 3qkt 3qku 4nch 4nci 4ncj 4nck

(-) Related Entries Specified in the PDB File

3qks 3qkt 3qku