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 :  CRYSTAL STRUCTURE OF PYRENE- AND PHENANTHRENE-MODIFIED DNA IN COMPLEX WITH THE BPUJ1 ENDONUCLEASE BINDING DOMAIN
 
Authors :  M. Probst, W. Aeschimann, T. -T. -H. Chau, S. M. Langenegger, A. Stocker
Date :  15 Jan 16  (Deposition) - 17 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B,C,D,L,M
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,L,M  (1x)
Keywords :  Phenanthrene, Pyrene, Dna, Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Probst, W. Aeschimann, T. T. Chau, S. M. Langenegger, A. Stocker, R. Haner
Structural Insight Into Dna-Assembled Oligochromophores: Crystallographic Analysis Of Pyrene- And Phenanthrene-Modified Dna In Complex With Bpuji Endonuclease.
Nucleic Acids Res. V. 44 7079 2016
PubMed-ID: 27422870  |  Reference-DOI: 10.1093/NAR/GKW644

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE R.BPUJI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BPUJIR
    Organism Scientific: BACILLUS PUMILUS
    Organism Taxid: 1408
 
Molecule 2 - DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
    Chains: L, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')
    Chains: M, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDLM
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  LM

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1YPE4Mod. Nucleotide4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YLDIHYDROGEN PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1YPE2Mod. Nucleotide4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YLDIHYDROGEN PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1YPE2Mod. Nucleotide4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YLDIHYDROGEN PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 5HLT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Cys A:37 -Pro A:38
2Phe A:115 -Pro A:116
3Cys B:37 -Pro B:38
4Phe B:115 -Pro B:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HLT)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......eee....eeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhh...eehhhhhhhh..hhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlt A   2 NYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSN 279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh...hhhhhhhhhhh........eee...eeeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlt B   2 NYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSN 279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        


Chain C from PDB  Type:DNA  Length:12
                                            
                 5hlt C 101 GxTACCCGTGGA 112
                             |     110  
                           102-YPE      


Chain D from PDB  Type:DNA  Length:12
                                            
                 5hlt D 201 TCCACGGGTAxC 212
                                   210| 
                                    211-YPE


Chain L from PDB  Type:DNA  Length:12
                                            
                 5hlt L 101 GxTACCCGTGGA 112
                             |     110  
                             |          
                           102-YPE      


Chain M from PDB  Type:DNA  Length:12
                                            
                 5hlt M 201 TCCACGGGTAxC 212
                                   210| 
                                    211-YPE
   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 5HLT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    YPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5hlt)
 
  Cis Peptide Bonds
    Cys A:37 - Pro A:38   [ RasMol ]  
    Cys B:37 - Pro B:38   [ RasMol ]  
    Phe A:115 - Pro A:116   [ RasMol ]  
    Phe B:115 - Pro B:116   [ 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
  5hlt
    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
  A3FMN7_BACPU | A3FMN7
    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
  A3FMN7_BACPU | A3FMN7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A3FMN7_BACPU | A3FMN7: 2vla 5hnf 5hnh

(-) Related Entries Specified in the PDB File

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