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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  BH-RNASEH:TCDA-DNA COMPLEX
 
Authors :  P. S. Pallan, M. Egli
Date :  05 Feb 14  (Deposition) - 11 Feb 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),D (1x)
Biol. Unit 2:  B (1x),C (1x),D (1x)
Keywords :  Bh Rnase-H:Dna Complex, Protein-Dna Complex, Rnase H, Ribonuclease H, Tricyclo Dna, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Egli, P. S. Pallan
Generating Crystallographic Models Of Dna Dodecamers From Structures Of Rnase H:Dna Complexes.
Methods Mol. Biol. V. 1320 111
PubMed-ID: 26227040  |  Reference-DOI: 10.1007/978-1-4939-2763-0_8

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A, C
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 59-196
    Gene: BH0863, RNHA
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Synonym: RNASE H
 
Molecule 2 - 5'-D(*CP*GP*CP*GP*AP*(TCY)P*TP*TP*CP*GP*CP*G)-3'
    Chains: B, D
    Engineered: YES
    Other Details: TCD-ADENINE DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x) D (1x)
Biological Unit 2 (1x):  B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TCY2Mod. Nucleotide(2R,3AS,4AR,5AR,5BS)-2-(6-AMINO-9H-PURIN-9-YL)-3A-HYDROXYHEXAHYDROCYCLOPROPA[4,5]CYCLOPENTA[1,2-B]FURAN-5A(4H)-YL DIHYDROGEN PHOSPHATE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2TCY-1Mod. Nucleotide(2R,3AS,4AR,5AR,5BS)-2-(6-AMINO-9H-PURIN-9-YL)-3A-HYDROXYHEXAHYDROCYCLOPROPA[4,5]CYCLOPENTA[1,2-B]FURAN-5A(4H)-YL DIHYDROGEN PHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2TCY-1Mod. Nucleotide(2R,3AS,4AR,5AR,5BS)-2-(6-AMINO-9H-PURIN-9-YL)-3A-HYDROXYHEXAHYDROCYCLOPROPA[4,5]CYCLOPENTA[1,2-B]FURAN-5A(4H)-YL DIHYDROGEN PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4OPJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:77 -Pro A:78
2Asn C:77 -Pro C:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OPJ)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4opj A  62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    71        81        91       101       111       121       131       141       151       161       171       181       191   


Chain B from PDB  Type:DNA  Length:12
                                            
                 4opj B   1 CGCGAaTTCGCG  12
                                 |  10  
                                 6-TCY  


Chain C from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4opj C  62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY 193
                                    71        81        91       101       111       121       131       141       151       161       171       181       191  


Chain D from PDB  Type:DNA  Length:12
                                            
                 4opj D   1 CGCGAaTTCGCG  12
                                 |  10  
                                 6-TCY
   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 4OPJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TCY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4opj)
 
  Cis Peptide Bonds
    Asn A:77 - Pro A:78   [ RasMol ]  
    Asn C:77 - Pro C:78   [ 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 | Biol. Unit 1 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
  4opj
    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
  RNH1_BACHD | Q9KEI9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.4
    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
  RNH1_BACHD | Q9KEI9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RNH1_BACHD | Q9KEI9: 1zbf 1zbi 1zbl 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3ey1 3i8d 3twh 3uld 4htu 4hue 4huf 4hug 4opk 5swm 5us2 5usa 5use 5usg 5w7n 5w7o

(-) Related Entries Specified in the PDB File

4opk