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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PF2046 IN COMPLEX WITH SSDNA
 
Authors :  J. S. Kim, K. Y. Hwang, W. C. Lee
Date :  10 Jul 15  (Deposition) - 10 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Rnaseh, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Kim, G. D. Sambalkhundev, S. H. Kim, A. Han, S. M. Ko, K. Y. Hwang, W. C. Lee
Structural Basis Of Two-Nucleotide Removal Of Ssdna By A Cryptic Rnase H Fold 3'-5' Exonuclease Pf2046 From Pyrococcus Furiosus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PF2046
    Gene: PF2046
    Organism Scientific: PYROCOCCUS FURIOSUS (STRAIN ATCC 43587 / DSM 3638 / JCM 8422 / VC1)
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
 
Molecule 2 - DNA (5'-D(P*TP*TP*TP*T)-3')
    Chains: D, E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , ASP A:80 , GLU A:145 , MG A:502 , HOH A:608 , DT D:7 , HOH D:102binding site for residue MG A 501
2AC2SOFTWAREASP A:7 , ASP A:80 , MG A:501 , HOH A:605 , HOH A:612 , DT D:6 , DT D:7binding site for residue MG A 502
3AC3SOFTWAREASP B:7 , THR B:8 , GLU B:61 , ASP B:80 , HOH B:415 , HOH B:417 , DT E:6 , DT E:7binding site for residue MG B 301
4AC4SOFTWAREASP B:7 , THR B:8 , GLU B:145 , DT E:7 , DT E:8binding site for residue MG B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:32 -Pro A:33
2Lys B:32 -Pro B:33
3Lys C:32 -Pro C:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CHI)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eee.....eeee.eeeeeee........eeeeee.........hhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....eeeeee..eeeeee.hhhhh..eeeee.......eeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5chi A   0 MMRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVPVRIAEIYAGIYSAKWGIENVEKEGHLIIGLPRYMEVNIKDGKIIGRSLDPREGGLYGSAEVSVPEGVKWEIYPNPVARRFMIFEIFSKR 229
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5chi B   0 MMRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVPVRIAEIYAGIYSAKWGIENVEKEGHLIIGLPRYMEVNIKDGKIIGRSLDPREGGLYGSAEVSVPEGVKWEIYPNPVARRFMIFEIFSK 228
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219         


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eee.....eeee.eeeeeee........eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee............hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhh.......eeee....eeeeee..eeeeee.hhhhh..eeeee........eeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5chi C   0 MMRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVPVRIAEIYAGIYSAKWGIENVEKEGHLIIGLPRYMEVNIKDGKIIGRSLDPREGGLYGSAEVSVPEGVKWEIYPNPVARRFMIFEIFS 227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        


Chain D from PDB  Type:DNA  Length:4
                                    
                 5chi D   5 TTTT   8


Chain E from PDB  Type:DNA  Length:4
                                    
                 5chi E   5 TTTT   8


Chain F from PDB  Type:DNA  Length:4
                                    
                 5chi F   5 TTTT   8
   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 5CHI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    MG  [ 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
    Lys A:32 - Pro A:33   [ RasMol ]  
    Lys B:32 - Pro B:33   [ RasMol ]  
    Lys C:32 - Pro C:33   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  5chi
    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
  Q8TZE9_PYRFU | Q8TZE9
    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
  Q8TZE9_PYRFU | Q8TZE9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8TZE9_PYRFU | Q8TZE9: 4o8u

(-) Related Entries Specified in the PDB File

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