Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE DRRECQ CATALYTIC CORE IN COMPLEX WITH ADP
 
Authors :  S. C. Chen, C. S. Yang, Y. Chen
Date :  14 Apr 14  (Deposition) - 20 May 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Unwinding, Topoisomerase, Helicase, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Chen, C. H. Huang, C. S. Yang, T. D. Way, M. C. Chang, Y. Chen
Crystal Structure Of Deinococcus Radiodurans Recq Helicase Catalytic Core Domain: The Interdomain Flexibility.
Biomed Res Int V. 2014 42725 2014
PubMed-ID: 25243132  |  Reference-DOI: 10.1155/2014/342725

(-) Compounds

Molecule 1 - DNA HELICASE RECQ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-517
    Gene: DR_1289
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:22 , ALA A:24 , PHE A:25 , ARG A:26 , GLN A:29 , GLY A:49 , GLY A:50 , GLY A:51 , LYS A:52 , SER A:53BINDING SITE FOR RESIDUE ADP A 601
2AC2SOFTWARECYS A:381 , CYS A:398 , CYS A:401 , CYS A:404BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWARETYR B:22 , ALA B:24 , ARG B:26 , GLN B:29 , THR B:48 , GLY B:49 , GLY B:50 , GLY B:51 , LYS B:52 , SER B:53BINDING SITE FOR RESIDUE ADP B 601
4AC4SOFTWARECYS B:381 , CYS B:398 , GLY B:399 , CYS B:401 , CYS B:404BINDING SITE FOR RESIDUE ZN B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q47)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:487 -His A:488
2Gly A:517 -Leu A:518
3Asn B:284 -Glu B:285
4Ser B:355 -Asp B:356
5Asp B:512 -Thr B:513

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q47)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q47)

(-) 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:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh......hhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh..eeeeee.hhhhhh..........hhhhhhhhhh....eeeee......hhhhhhhhh......eee.......eeeeeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeee..........eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhh.........hhhhhhhhhhhhhhh..eee.....eee..hhhhhhh.....eeehhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q47 A   5 PAALHDRALHLLQTIWGYPAFRGVQGEIVQQVAEGGNALVLMPTGGGKSLCYQLPSLLRPGTGIVVSPLIALMKDQVDTLRQNGVRAAFLNSTLLPHEAREVEDALLRGDLDLLYVAPERLLMPRTLDLLERAPVALFAIDEAHCVSQWGHDFRPEYQQLSVLAERFPELPRVALTATADERTRADIKSVLRLEDAPQFVSSFDRPNIQYRVGLKDSPKTQLLHFIREEHPGDAGIVYCLSRKSVEETAKWLQAQGIDALAYHAGLSSTERNNVQERFLNEEGVIVCATVAIDKPNVRFVAHLDLPKSMEGYYQETGRAGRDGLPSTAWMVYGLSDVVNVRRMLAQSDAPEEVKRVEASKLDALLTYCEAATCRRQVLLHYFGEELSEPCGNCDVCLNPPRVRDLTREAQMALSATIRTGNRFGAAHLTDVLLGRETDKVLAQGHHQLPTFGVGKEHDEKLWRSVLRQLVSLGYLSADDHFGLRATGKSRGILKEGQKLLLREDTLLPGLEHH 521
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294||     308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518   
                                                                                                                                                                                                                                                                                                                            295|                                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                             300                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeehhhhhh...hhhhhhh..eeeeee.hhhhhh.......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh......eee.......eeeeeee..hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.....eee........hhhhhhhhhh.....eeee.........eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhh.........hhhhhhhhhhhhhhh..eeee...eeee...hhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q47 B   8 LHDRALHLLQTIWGYPAFRGVQGEIVQQVAEGGNALVLMPTGGGKSLCYQLPSLLRPGTGIVVSPLIALMKDQVDTLRQNGVRAAFLNSTLLPHEAREVEDALLRGDLDLLYVAPERLLMPRTLDLLERAPVALFAIDEAHCVSQWGHDFRPEYQQLSVLAERFPELPRVALTATADERTRADIKSVLRLEDAPQFVSSFDRPNIQYRVGLKDSPKTQLLHFIREEHPGDAGIVYCLSRKSVEETAKWLQAQGIDALAYHAGLSSTERNNVQERFLNEEGVIVCATVADKPNVRFVAHLDLPKSMEGYYQETGRAGRDGLPSTAWMVYGLSDVVNVRRMLAQSDAPEEVKRVEASKLDALLTYCEAATCRRQVLLHYFGEELSEPCGNCDVCLNPPRVRDLTREAQMALSATIRTGNRFGAAHLTDVLLGRETDKVLAQGHHQLPTFGVGKEHDEKLWRSVLRQLVSLGYLSADDHFGLRATGKSRGILKEGQKLLLREDTL 514
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512  
                                                                                                                                                                                                                                                                                                                         295|                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                          301
   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 4Q47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q47)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:284 - Glu B:285   [ RasMol ]  
    Asp A:487 - His A:488   [ RasMol ]  
    Asp B:512 - Thr B:513   [ RasMol ]  
    Gly A:517 - Leu A:518   [ RasMol ]  
    Ser B:355 - Asp B:356   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4q47
    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
  Q9RUU2_DEIRA | Q9RUU2
    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
  Q9RUU2_DEIRA | Q9RUU2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RUU2_DEIRA | Q9RUU2: 2ma1 2rhf 4q48

(-) Related Entries Specified in the PDB File

1oyw ECRECQ
2v1x HRECQ1
4q48