Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  ATP-GAMMA-S BOUND RAD50 FROM CHAETOMIUM THERMOPHILUM IN COMPLEX WITH DNA
 
Authors :  F. U. Seifert, K. Lammens, G. Stoehr, B. Kessler, K. -P. Hopfner
Date :  19 Aug 15  (Deposition) - 02 Mar 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Atpase, Atpys Bound, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. U. Seifert, K. Lammens, G. Stoehr, B. Kessler, K. P. Hopfner
Structural Mechanism Of Atp-Dependent Dna Binding And Dna End Bridging By Eukaryotic Rad50.
Embo J. V. 35 759 2016
PubMed-ID: 26896444  |  Reference-DOI: 10.15252/EMBJ.201592934

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN,PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTHT_0073630
    Mutation: YES
    Organism Scientific: CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM DSM 1495
    Organism Taxid: 759272
 
Molecule 2 - DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)- 3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1AES2Ligand/Ion4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:41 , GLN A:159 , AGS A:1402 , HOH A:1517 , HOH A:1524binding site for residue MG A 1401
2AC2SOFTWAREARG A:13 , SER A:14 , ASN A:36 , GLY A:37 , SER A:38 , GLY A:39 , LYS A:40 , THR A:41 , THR A:42 , ALA A:64 , ILE A:66 , ASP A:68 , GLN A:159 , HIS A:1275 , ARG A:1297 , MG A:1401 , HOH A:1506 , HOH A:1517 , HOH A:1524 , ASP B:1164 , MET B:1201 , ARG B:1206 , SER B:1208 , ALA B:1209 , GLY B:1210 , GLN B:1211binding site for residue AGS A 1402
3AC3SOFTWARETHR A:1151 , GLU A:1225 , ILE A:1258 , ARG A:1262binding site for residue AES A 1403
4AC4SOFTWARETHR B:41 , GLN B:159 , AGS B:1402 , HOH B:1504 , HOH B:1512binding site for residue MG B 1401
5AC5SOFTWAREASP A:1164 , MET A:1194 , ARG A:1206 , SER A:1208 , ALA A:1209 , GLY A:1210 , GLN A:1211 , ARG B:13 , SER B:14 , ASN B:36 , GLY B:37 , SER B:38 , GLY B:39 , LYS B:40 , THR B:41 , THR B:42 , ALA B:64 , ILE B:66 , HIS B:67 , ASP B:68 , GLN B:159 , HIS B:1275 , ARG B:1297 , MG B:1401 , HOH B:1504 , HOH B:1508 , HOH B:1512 , HOH B:1525binding site for residue AGS B 1402
6AC6SOFTWAREGLU B:1154 , GLU B:1225 , ARG B:1262 , HOH B:1552binding site for residue AES B 1403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:27 -Pro A:28
2Thr B:27 -Pro B:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DAC)

(-) 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:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..........eeee....eeeee.....hhhhhhhhhhhhhhh..............hhhhhh..eeeeeeeeeee.....eeeeeeeeeeee.....eeeee...eeeeee..eeeeee.hhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....ee...ee..eeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh..eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dac A    2 SKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYATTGELPPNSTRNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQLLVQRNNKRTQKTLEGSLLLRNNGERTVISTRVAELDKLVSEKLGVPPAILDAVIFCHQDDSLWPMSEPAALKKRFDEIFEAQKYTKVIENIRLLKKKKGDELKILKEREVQDKANKERAEDLKDAKAKYKETHIKVETTKAAIEDLGRGMAAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDIDTIQIRSDVESTTSSDSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAESFCANCGLIALDQPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEFLKYMQCSDFCDDFYRVKRDEKQNSVIVRESITR 1312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|     1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310  
                                                                                                                                                                                                                                                     221|                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                     1101                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..........eeee....eeeee.....hhhhhhhhhhhhhhh..............hhhhhh..eeeeeeeeeee.....eeeeeeeeeeee.....eeeee...eeeeee..eeeeee.hhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee...eeeeeeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh..eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dac B    2 SKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYATTGELPPNSTRNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQLLVQRNNKRTQKTLEGSLLLRNNGERTVISTRVAELDKLVSEKLGVPPAILDAVIFCHQDDSLWPMSEPAALKKRFDEIFEAQKYTKVIENIRLLKKKKGDELKILKEREVQDKANKERAELDLKDAKAKYKETHIKVETTKAAIEDLGRGMAAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDIDTIQIRSDVESTTSSDSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAESFCANCGLIALDQPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEFLKYMQCSDFCDDFYRVKRDEKQNSVIVRESIT 1311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|     1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309  
                                                                                                                                                                                                                                                     221|                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                     1100                                                                                                                                                                                                                   


Chain C from PDB  Type:DNA  Length:15
                                                
                5dac C    1 CCCCCCCCCCCCCCC   15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                                
                5dac D    1 GGGGGGGGGGGGGGG   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 5DAC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AGS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:27 - Pro A:28   [ RasMol ]  
    Thr B:27 - Pro B:28   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dac
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  G0SHW7_CHATD | G0SHW7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  G0SHW7_CHATD | G0SHW7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G0SHW7_CHATD | G0SHW7: 5da9

(-) Related Entries Specified in the PDB File

5da9