Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCELIOPHTHORA THERMOPHILA RAD26 (RESIDUES 373-841)
 
Authors :  K. R. Andersen
Date :  09 Aug 16  (Deposition) - 29 Mar 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rad26 (Atrip), Rad3 (Atr), Dna-Damage Response (Ddr), Kinase Signaling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. R. Andersen
Insights Into Rad3 Kinase Recruitment From The Crystal Structure Of The Dna Damage Checkpoint Protein Rad26.
J. Biol. Chem. V. 292 8149 2017
PubMed-ID: 28314775  |  Reference-DOI: 10.1074/JBC.M117.780189

(-) Compounds

Molecule 1 - RAD26
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    Expression System VariantLOBSTR
    FragmentUNP RESIDUES 373-841
    GeneMYCTH_2305697
    Organism ScientificMYCELIOPHTHORA THERMOPHILA ATCC 42464
    Organism Taxid573729

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5LOI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LOI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LOI)

(-) 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.................hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5loi A 374 PDFLKLFLNHTPTFDmFSRFCFPSDPERSLASIVLQKLPQmGSPGDPTSLLVDFADTLIDLWHQCLSERYYGPIYHLVSLLLYTLDLNAVEVAPHILSSLIPVCATTCRLVALPRLNSADGDLSGHPDAVVRQLCLNIDVTQCLSVLYLAASGCLPQPLPQDTPQLEFWKTmELDFVLTmLSPKNPEEDWSAmmILLRTSVAPHSIGPIPSSATNSTNRRSEAKNADAVAATLIDCVSSFLCEPPKWATPRSAKEIAARLAALRTLmAFATGHFGARQIAESDVAIPRLVTVLCWALDRLYDSDLPPDSmSLLHQIIAQGTRLLHFLVTDHRTSDAANISTKLAASHGGSQRYFLTLARLNFAEEDLVLEAGIDAETVELAHELLELAVTP 831
                                   383||   | 399       409       419|      429       439       449       459       469       479       489       499       509       519       529       547       557 |     567       577  ||   587       597       607       617       627       637       647      |657       667       677       687     ||750       760       770       780       790       800       810       820       830 
                                    384|   |                      420-MSE                                                                                                               538|         559-MSE 567-MSE      580-MSE                                                                   654-MSE                                693|  |                                                                                 
                                     391   |                                                                                                                                             547                               581-MSE                                                                                                          747  |                                                                                 
                                         395-MSE                                                                                                                                                                                                                                                                                               750-MSE                                                                             

   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 5LOI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5LOI)

 Visualization

(-) Interactive Views

Asymmetric 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5loi)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5loi)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5loi
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  G2QDY6_MYCTT | G2QDY6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  G2QDY6_MYCTT | G2QDY6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5LOI)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LOI)